Proteopedia - User contributions [en]

User:Karsten Theis/Sandbox 1

2025-10-12T02:35:24Z

Karsten Theis:

<applet size='[450,338]' frame='true' align='right'
scene='User:Karsten_Theis/Sandbox_1/Globe3/2'
caption='UvrB' />

<ref>DOI:10.1002/open.201300012</ref>

Here is the <scene name='49/491982/Pentane/1'>pentane</scene> molecule. Here is how it can rotate around its single bonds to get a different conformation:

<jmol>
<jmolLink>
<script> var a = [1,2,3,4,5,6,7,8,9,10]; var b = [1,2,3,4,5,6,7,8,9,10]; for(var i IN a) {for(var i IN b){set refreshing false; rotate branch {C3}{C4} 5; rotate branch {C3}{C2} 2; set refreshing true; delay 0.05}}
</script>
<text>rotate</text>
</jmolLink>
</jmol>

<jmol>
<jmolLink>
<script> load $pentane; rotate BRANCH [1 2 3 4 0 900 3 2 1 0 1800 0] 10
</script>
<text>Simpler, single command script</text>
</jmolLink>
</jmol>

load $pentane; rotate BRANCH [1 2 3 4 0 900 3 2 1 0 1800 0] 10

For large structures, use label "%D" to find numbers of selected atoms.

Metallorganic framework <scene name='49/491982/Mof_hexagonal/1'>hexagonal</scene> or cubic

<scene name='User:Karsten_Theis/Sandbox_1/Globe2/1'>Proteopedia</scene>

<scene name='User:Karsten_Theis/Sandbox_1/Fig1/1'>UvrB</scene>

<scene name='User:Karsten_Theis/Sandbox_1/Globe3/1'>Fancy</scene>

<scene name='49/491982/Proinsulin/1'>insulin</scene>

<scene name='49/491982/Proinsulin/6'>insulin surface</scene>

<scene name='49/491982/Amyloid_stack_2m5n/2'>amyloid aggregate</scene>

<scene name='49/491982/1bna/1'>DNA</scene>

<scene name='49/491982/1bna/3'>DNA different orientation</scene>

<jmol>
<jmolLink>
<script> slab on; var a = [1,2,3,4,5,6,7,8]; for(var i IN a) {isosurface translucent @i; delay 0.4;}
</script>
<text>Fade surface to invisible</text>
</jmolLink>
</jmol> (basic)

== Table ==

<table>
<tr>
<td>[http://www.google.com W2]<br> [[Image:Insulin.gif|link=Insulin]]</td>
<td>[[Image:Insulin.gif]]</td>
<td>[[Image:Insulin.gif]]</td>
</tr>
<tr>
<td>[[Image:Insulin.gif]]</td>
<td>[[Image:Insulin.gif]]</td>
<td>[[Image:Insulin.gif]]</td>
</tr>
<tr>
<td>[[Image:Insulin.gif]]</td>
<td>[[Image:Insulin.gif]]</td>
<td>[[Image:Insulin.gif]]</td>
</tr>
</table>

== References ==
<references/>

File:MOFhexagonal.png

2025-10-12T02:27:50Z

Karsten Theis: CSD Entry: QEKBAK

== Summary ==
CSD Entry: QEKBAK
== Licensing ==
{{self|cc-by-sa-3.0}}

Jmol/Superposition

2025-07-07T15:37:30Z

Karsten Theis:

==Introduction==
This page is a tutorial on how to superimpose two structures in Jmol and show them in Proteopedia. Superpositions (or overlays) are a way to compare two structures by moving them on top of one another so the [[Superposition_with_jmol#Equivalent_atoms|"equivalent atoms"]] are close to one another. Because the two structures are different, not all equivalent atoms can match at the same time. Instead, you minimize the root-mean-square of the distances (RMSD) to achieve a compromise. If you want to see superpositions in the context of a Proteopedia page (and look at the underlying Jmol scripts), take a look at [[Garman lab: Interconversion of lysosomal enzyme specificities]] and [[Schubert lab: bacterial InIC disrupts human Tuba complexes]].

==Loading two structures==
Before you can superimpose two structures in Jmol, they have to be loaded at the same time. The "load files" command accomplishes that. In the following, the related structures with the PDB IDs 3HG5 and 3H54 are loaded:
<nowiki>
load files "=3HG5" "=3H54"
model 0</nowiki>
Once they are loaded, you refer to them as "1.1" and "2.1". The number before the decimal point refers to the two structures, while the "1" after the decimal point refers to the first model in the respective coordinate set. (If you want to superimpose different parts of a single structure, for example the two subunits in a dimer, you just load one structure, and access the subunits via the chain identifier - examples will follow). The model command determines which model will be displayed (0 means all).

==Equivalent atoms==
You have to choose which sets of atoms should be superimposed, i.e. the distances of which pairs of atoms should be minimized. In this example, we choose the alpha carbons of the respective active sites, but other choices are possible. In Jmol, you need two atom selection expressions, one for each structure. Because you want pairs of equivalent atoms, the number of atoms selected in the first structure should be equal to the number of atoms selected in the second set. In our example, we first define two atom selections, and then use these later.
<nowiki>
# define active site C-alpha atoms
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A.CA
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A.CA</nowiki>

If you don't know which atoms to superimpose, or if you don't even know which other structure is similar to the one of interest, you can do a [[Structural alignment tools|structural alignment]] first. The output will tell you which structures show similarity to the one of interest, and it will show a list of equivalent atoms (usually it just considers C-alpha atoms for protein structures). Historically, [https://en.wikipedia.org/wiki/Jane_S._Richardson Jane Richardson's] beautiful [https://en.wikipedia.org/wiki/Ribbon_diagram ribbon diagrams] played an important role in detecting structural similarities through human pattern recognition ("This cartoon looks similar to another structure I saw previously").

If you know which residues you want to target for superposition because you have a multiple sequence alignment, you can go to [https://github.com/fomightez/cl_demo-binder here], press a `launch binder` badge to launch an active Jupyter session in your browser and then select from the index of notebooks 'Determine residues that match to a reference from multiple sequence alignment and use to construct fit commands' to work through a Jupyter notebook that steps process of using a multiple sequence alignment to determine residues that are expected to be equivalents and then at the bottom of the section generates Jmol commands. You can substitute your own alignment and structure of interest once you follow how it works.

==Compare command==
The Jmol command to superimpose structures is called "compare", and it has a lot of parameters. Here is an example:
<nowiki>
compare {2.1} {1.1} ATOMS {~actnagal} {~actgal} ROTATE TRANSLATE
</nowiki>
The first two parameters "{2.1}{1.1}" define which atoms will be affected by the superposition. Here, we choose all of the atoms in the two structures. Next, the atom selections after the "ATOMS" keyword define which equivalent pairs of atoms. Here, we are using the atoms selections previously defined, but you can also use atom selections on the fly. Within these selections, atoms will be paired up in order (first atom in first selection pairs with first atom in second selection, ..., N-th atom in first selection pairs with N-th atom in second selection). If this is not the pairing you want, you can split up the selection and add more selection statements, i.e. something like "{selection A of structure 1}{selection A of structure 2}{selection B of structure 1}{selection B of structure 2}...".

Finally, the "ROTATE TRANSLATE" keywords do the actual superposition, i.e. change the coordinates of the first structure (in our case all coordinates of the single model in the second structure because we specified this with the first parameter "2.1"). This change of parameters is permanent, so for all following commands displaying structures, the coordinates will be superimposed.

If the superposition is successful, the root mean square distance (RMSD) of matching atoms will be displayed in the console. If there is no output, the superposition failed (e.g. if less than 3 atoms are selected).

==Displaying the superposed structures==
Once the structures are superimposed, you can show them using the usual selection and drawing commands. To avoid selecting atoms from the second structure by accident when you just want atoms from the first structure, the easiest is to add a "and 1.1" to your selections. Here is an example of two separate sets of commands to draw a cartoon of the first structure in green and the second in blue.
<nowiki>
model 0
select protein and 1.1; cartoon; color palegreen; center selected
select protein and 2.1; cartoon; color cornflowerblue;</nowiki>

==Troubleshooting==
Jmol does not alert you if your sets of equivalent atoms used in a superposition contain different number of atoms. Let's say you made a mistake in your selection and the first atom set contains 50 atoms and the second contains 51. Jmol will just ignore the last atom in the second set. However, your mistake might have messed up the pairing of atoms you intended. The only feedback Jmol gives is the so-called RMSD (the root-mean-square distance of equivalent atom pairs). You can also check if your superposition makes sense by displaying both structures, and checking if equivalent atoms are close to each other.

If something did go awry, an efficient way of troubleshooting is to list the selected atoms. Whenever you select atoms, Jmol tells you how many atoms are selected. The command "show selection" shows a list of all the selected atoms. If you put both lists side by side, the intended equivalent atom pairs should line up.

<nowiki>
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A.CA
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A.CA
select ~actgal
show selected
select ~actnagal
show selected</nowiki>

Here is the output:
<nowiki>
structure 1 structure 2
13 atoms selected 13 atoms selected
[TRP]47:A.CA/1.1 #119 [TRP]33:A.CA/2.1 #115
[ASP]92:A.CA/1.1 #489 [ASP]78:A.CA/2.1 #496
[ASP]93:A.CA/1.1 #497 [ASP]79:A.CA/2.1 #504
[TYR]134:A.CA/1.1 #826 [TYR]119:A.CA/2.1 #814
[CYS]142:A.CA/1.1 #886 [CYS]127:A.CA/2.1 #877
[LYS]168:A.CA/1.1 #1086 [LYS]154:A.CA/2.1 #1088
[ASP]170:A.CA/1.1 #1106 [ASP]156:A.CA/2.1 #1105
[CYS]172:A.CA/1.1 #1118 [CYS]158:A.CA/2.1 #1117
[GLU]203:A.CA/1.1 #1358 [SER]188:A.CA/2.1 #1338
[LEU]206:A.CA/1.1 #1388 [ALA]191:A.CA/2.1 #1365
[TYR]207:A.CA/1.1 #1396 [TYR]192:A.CA/2.1 #1370
[ARG]227:A.CA/1.1 #1587 [ARG]213:A.CA/2.1 #1550
[ASP]231:A.CA/1.1 #1622 [ASP]217:A.CA/2.1 #1589
</nowiki>

It shows that even though the residue numbers are different within the pairs, most pairs have matching residue types, supporting the notion that atoms are indeed equivalent. (Exceptions are Glu203 vs Ser188, and Leu206 vs Ala 191, which do occupy equivalent positions in the active site but are responsible for different substrate specificities of the two enzymes). This method is excellent for spotting problems like typos, problems related to missing residues in one or the other structure, alternate conformations (i.e. selecting two C-alpha atoms for a single residue), etc.

The [[Image:storymorph.spt | storymorph]] suite of functions has two ways to check selections. "atom_order(sel1, sel2)" prints the selected atoms in the two sets side-by-side. The function "matched_residues(sel1, sel2)" goes through all residue numbers and says whether both selections contain the same number of atoms of a given residue number.

The [[Jmol/Storymorph#Helper_functions|Storymorph]] scripts contain helper functions mathed_residues and atom_order that make troubleshooting easier.

==Demonstration==
<StructureSection load='3hg5' size='340' side='right' caption='' scene=''>
The initial scene is one of the two example structures, 3HG5. Click on the green link to see the <scene name='79/794960/Test/4'>superposition</scene> of 3HG5 and 3H54 resulting from the example code above. It is nice to offer views of just one or the other structure, or animate the scene go back and forth. This makes it easier to examine the structures.
<jmol>
<jmolButton>
<script>!exit; delay 1.2; model 1</script>
<text>structure 1</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>!exit; delay 1.5; model 2</script>
<text>structure 2</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>!exit; delay 1.5; model 0</script>
<text>both</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>animation mode loop; animation on</script>
<text>animate</text>
</jmolButton>
</jmol>

The four buttons above were created with the following script:

<nowiki>
<jmol>
<jmolButton>
<script>!exit; delay 1.2; model 1</script>
<text>structure 1</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>!exit; delay 1.5; model 2</script>
<text>structure 2</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>!exit; delay 1.5; model 0</script>
<text>both</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>animation mode loop; animation on</script>
<text>animate</text>
</jmolButton>
</jmol></nowiki>

===Superposition of atoms within a single structure===
We can also do a superposition of the two subunits in the dimer of a single structure, say <scene name='79/794960/Dimer_intact/1'>3HG5</scene>.

You can see an animation of the superposition by clicking on the button below (to get back to the dimer, click on the green link above):
<jmol>
<jmolButton>
<script>compare {*:A} {*:B} SUBSET{*.CA} ATOMS{protein}{protein} ROTATE TRANSLATE 2.0</script>
<text>Superimpose!</text>
</jmolButton>
</jmol>

The resulting scene is <scene name='79/794960/Dimer_difference/1'>here</scene> and the commands used to make this figure are below.

<nowiki>
load 3HG5
compare {*:A} {*:B} SUBSET{*.CA} ATOMS{protein}{protein} ROTATE TRANSLATE
select all; center selected
cartoon only
</nowiki>

This script compares (and superimposes) all C-alpha atoms of chain A with all of chain B. This script would not do a good job if - say - the first couple residues were missing in chain A but not in chain B (because the atom pairs would not be matched up correctly). In our case, however, each subunit has the same residues in the same order, so it works nicely.

</StructureSection>

If you need a console:
<jmol>
<jmolButton>
<script> console;
</script>
<text>console</text>
</jmolButton>
</jmol>

Jmol/Superposition

2025-07-07T15:35:09Z

Karsten Theis:

==Introduction==
This page is a tutorial on how to superimpose two structures in Jmol and show them in Proteopedia. Superpositions (or overlays) are a way to compare two structures by moving them on top of one another so the [[Superposition_with_jmol#Equivalent_atoms|"equivalent atoms"]] are close to one another. Because the two structures are different, not all equivalent atoms can match at the same time. Instead, you minimize the root-mean-square of the distances (RMSD) to achieve a compromise. If you want to see superpositions in the context of a Proteopedia page (and look at the underlying Jmol scripts), take a look at [[Garman lab: Interconversion of lysosomal enzyme specificities]] and [[Schubert lab: bacterial InIC disrupts human Tuba complexes]].

==Loading two structures==
Before you can superimpose two structures in Jmol, they have to be loaded at the same time. The "load files" command accomplishes that. In the following, the related structures with the PDB IDs 3HG5 and 3H54 are loaded:
<nowiki>
load files "=3HG5" "=3H54"
model 0</nowiki>
Once they are loaded, you refer to them as "1.1" and "2.1". The number before the decimal point refers to the two structures, while the "1" after the decimal point refers to the first model in the respective coordinate set. (If you want to superimpose different parts of a single structure, for example the two subunits in a dimer, you just load one structure, and access the subunits via the chain identifier - examples will follow). The model command determines which model will be displayed (0 means all).

==Equivalent atoms==
You have to choose which sets of atoms should be superimposed, i.e. the distances of which pairs of atoms should be minimized. In this example, we choose the alpha carbons of the respective active sites, but other choices are possible. In Jmol, you need two atom selection expressions, one for each structure. Because you want pairs of equivalent atoms, the number of atoms selected in the first structure should be equal to the number of atoms selected in the second set. In our example, we first define two atom selections, and then use these later.
<nowiki>
# define active site C-alpha atoms
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A.CA
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A.CA</nowiki>

If you don't know which atoms to superimpose, or if you don't even know which other structure is similar to the one of interest, you can do a [[Structural alignment tools|structural alignment]] first. The output will tell you which structures show similarity to the one of interest, and it will show a list of equivalent atoms (usually it just considers C-alpha atoms for protein structures). Historically, [https://en.wikipedia.org/wiki/Jane_S._Richardson Jane Richardson's] beautiful [https://en.wikipedia.org/wiki/Ribbon_diagram ribbon diagrams] played an important role in detecting structural similarities through human pattern recognition ("This cartoon looks similar to another structure I saw previously").

If you know which residues you want to target for superposition because you have a multiple sequence alignment, you can go to [https://github.com/fomightez/cl_demo-binder here], press a `launch binder` badge to launch an active Jupyter session in your browser and then select from the index of notebooks 'Determine residues that match to a reference from multiple sequence alignment and use to construct fit commands' to work through a Jupyter notebook that steps process of using a multiple sequence alignment to determine residues that are expected to be equivalents and then at the bottom of the section generates Jmol commands. You can substitute your own alignment and structure of interest once you follow how it works.

==Compare command==
The Jmol command to superimpose structures is called "compare", and it has a lot of parameters. Here is an example:
<nowiki>
compare {2.1} {1.1} ATOMS {~actnagal} {~actgal} ROTATE TRANSLATE
</nowiki>
The first two parameters "{2.1}{1.1}" define which atoms will be affected by the superposition. Here, we choose all of the atoms in the two structures. Next, the atom selections after the "ATOMS" keyword define which equivalent pairs of atoms. Here, we are using the atoms selections previously defined, but you can also use atom selections on the fly. Within these selections, atoms will be paired up in order (first atom in first selection pairs with first atom in second selection, ..., N-th atom in first selection pairs with N-th atom in second selection). If this is not the pairing you want, you can split up the selection and add more selection statements, i.e. something like "{selection A of structure 1}{selection A of structure 2}{selection B of structure 1}{selection B of structure 2}...".

Finally, the "ROTATE TRANSLATE" keywords do the actual superposition, i.e. change the coordinates of the first structure (in our case all coordinates of the single model in the second structure because we specified this with the first parameter "2.1"). This change of parameters is permanent, so for all following commands displaying structures, the coordinates will be superimposed.

If the superposition is successful, the root mean square distance (RMSD) of matching atoms will be displayed in the console. If there is no output, the superposition failed (e.g. if less than 3 atoms are selected).

==Displaying the superposed structures==
Once the structures are superimposed, you can show them using the usual selection and drawing commands. To avoid selecting atoms from the second structure by accident when you just want atoms from the first structure, the easiest is to add a "and 1.1" to your selections. Here is an example of two separate sets of commands to draw a cartoon of the first structure in green and the second in blue.
<nowiki>
model 0
select protein and 1.1; cartoon; color palegreen; center selected
select protein and 2.1; cartoon; color cornflowerblue;</nowiki>

==Troubleshooting==
Jmol does not alert you if your sets of equivalent atoms used in a superposition contain different number of atoms. Let's say you made a mistake in your selection and the first atom set contains 50 atoms and the second contains 51. Jmol will just ignore the last atom in the second set. However, your mistake might have messed up the pairing of atoms you intended. The only feedback Jmol gives is the so-called RMSD (the root-mean-square distance of equivalent atom pairs). You can also check if your superposition makes sense by displaying both structures, and checking if equivalent atoms are close to each other.

If something did go awry, an efficient way of troubleshooting is to list the selected atoms. Whenever you select atoms, Jmol tells you how many atoms are selected. The command "show selection" shows a list of all the selected atoms. If you put both lists side by side, the intended equivalent atom pairs should line up.

<nowiki>
define ~actgal 1.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A.CA
define ~actnagal 2.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A.CA
select ~actgal
show selected
select ~actnagal
show selected</nowiki>

Here is the output:
<nowiki>
structure 1 structure 2
13 atoms selected 13 atoms selected
[TRP]47:A.CA/1.1 #119 [TRP]33:A.CA/2.1 #115
[ASP]92:A.CA/1.1 #489 [ASP]78:A.CA/2.1 #496
[ASP]93:A.CA/1.1 #497 [ASP]79:A.CA/2.1 #504
[TYR]134:A.CA/1.1 #826 [TYR]119:A.CA/2.1 #814
[CYS]142:A.CA/1.1 #886 [CYS]127:A.CA/2.1 #877
[LYS]168:A.CA/1.1 #1086 [LYS]154:A.CA/2.1 #1088
[ASP]170:A.CA/1.1 #1106 [ASP]156:A.CA/2.1 #1105
[CYS]172:A.CA/1.1 #1118 [CYS]158:A.CA/2.1 #1117
[GLU]203:A.CA/1.1 #1358 [SER]188:A.CA/2.1 #1338
[LEU]206:A.CA/1.1 #1388 [ALA]191:A.CA/2.1 #1365
[TYR]207:A.CA/1.1 #1396 [TYR]192:A.CA/2.1 #1370
[ARG]227:A.CA/1.1 #1587 [ARG]213:A.CA/2.1 #1550
[ASP]231:A.CA/1.1 #1622 [ASP]217:A.CA/2.1 #1589
</nowiki>

It shows that even though the residue numbers are different within the pairs, most pairs have matching residue types, supporting the notion that atoms are indeed equivalent. (Exceptions are Glu203 vs Ser188, and Leu206 vs Ala 191, which do occupy equivalent positions in the active site but are responsible for different substrate specificities of the two enzymes). This method is excellent for spotting problems like typos, problems related to missing residues in one or the other structure, alternate conformations (i.e. selecting two C-alpha atoms for a single residue), etc.

The [[Image:storymorph.spt | storymorph]] suite of functions has two ways to check selections. "atom_order(sel1, sel2)" prints the selected atoms in the two sets side-by-side. The function "matched_residues(sel1, sel2)" goes through all residue numbers and says whether both selections contain the same number of atoms of a given residue number.

The [[Jmol/Storymorph#Helper_functions|Storymorph]] scripts contain helper functions mathed_residues and atom_order that make troubleshooting easier.

==Demonstration==
<StructureSection load='3hg5' size='340' side='right' caption='' scene=''>
The initial scene is one of the two example structures, 3HG5. Click on the green link to see the <scene name='79/794960/Test/3'>superposition</scene> of 3HG5 and 3H54 resulting from the example code above. It is nice to offer views of just one or the other structure, or animate the scene go back and forth. This makes it easier to examine the structures.
<jmol>
<jmolButton>
<script>!exit; delay 1.2; model 1</script>
<text>structure 1</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>!exit; delay 1.5; model 2</script>
<text>structure 2</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>!exit; delay 1.5; model 0</script>
<text>both</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>animation mode loop; animation on</script>
<text>animate</text>
</jmolButton>
</jmol>

The four buttons above were created with the following script:

<nowiki>
<jmol>
<jmolButton>
<script>!exit; delay 1.2; model 1</script>
<text>structure 1</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>!exit; delay 1.5; model 2</script>
<text>structure 2</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>!exit; delay 1.5; model 0</script>
<text>both</text>
</jmolButton>
</jmol>
<jmol>
<jmolButton>
<script>animation mode loop; animation on</script>
<text>animate</text>
</jmolButton>
</jmol></nowiki>

===Superposition of atoms within a single structure===
We can also do a superposition of the two subunits in the dimer of a single structure, say <scene name='79/794960/Dimer_intact/1'>3HG5</scene>.

You can see an animation of the superposition by clicking on the button below (to get back to the dimer, click on the green link above):
<jmol>
<jmolButton>
<script>compare {*:A} {*:B} SUBSET{*.CA} ATOMS{protein}{protein} ROTATE TRANSLATE 2.0</script>
<text>Superimpose!</text>
</jmolButton>
</jmol>

The resulting scene is <scene name='79/794960/Dimer_difference/1'>here</scene> and the commands used to make this figure are below.

<nowiki>
load 3HG5
compare {*:A} {*:B} SUBSET{*.CA} ATOMS{protein}{protein} ROTATE TRANSLATE
select all; center selected
cartoon only
</nowiki>

This script compares (and superimposes) all C-alpha atoms of chain A with all of chain B. This script would not do a good job if - say - the first couple residues were missing in chain A but not in chain B (because the atom pairs would not be matched up correctly). In our case, however, each subunit has the same residues in the same order, so it works nicely.

</StructureSection>

If you need a console:
<jmol>
<jmolButton>
<script> console;
</script>
<text>console</text>
</jmolButton>
</jmol>

User:Karsten Theis/T7RNAP physical model explanation

2025-06-20T02:46:22Z

Karsten Theis:

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[Image:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. To assemble it, you bring the two flat sides together (the view is a "butterflied" version of the structure). On the left is the N-terminal part (roughly) with the nucleic acid forming a transcription bubble. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm. For an annotated image, see below.

[[Image:1msw legend.png|800px]]

<StructureSection load='' size='340' side='right' caption='' scene='10/1081719/T7_rnap/2'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/2'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 3.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 3.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 3.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 3.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 3.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>select protein; cartoon off; spacefill off; backbone 0.5</script>
<text>alpha trace</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

User:Karsten Theis/T7RNAP physical model explanation

2025-06-20T02:45:07Z

Karsten Theis:

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[Image:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. To assemble it, you bring the two flat sides together (the view is a "butterflied" version of the structure). On the left is the N-terminal part (roughly) with the nucleic acid forming a transcription bubble. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm. For an annotated image, see below.

[[Image:1msw legend.png|800px]]

<StructureSection load='' size='340' side='right' caption='' scene='10/1081719/T7_rnap/2'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/2'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 5.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 5.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 5.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 5.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 5.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>select protein; cartoon off; spacefill off; backbone 0.5</script>
<text>alpha trace</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

User:Karsten Theis/T7RNAP physical model explanation

2025-06-20T02:43:42Z

Karsten Theis:

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[Image:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. To assemble it, you bring the two flat sides together (the view is a "butterflied" version of the structure). On the left is the N-terminal part (roughly) with the nucleic acid forming a transcription bubble. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm. For an annotated image, see below.

[[Image:1msw legend.png|800px]]

<StructureSection load='' size='340' side='right' caption='' scene='10/1081719/T7_rnap/2'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/2'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>select protein; cartoon off; spacefill off; backbone 0.5</script>
<text>alpha trace</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

User:Karsten Theis/T7RNAP physical model explanation

2025-06-20T02:41:55Z

Karsten Theis:

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[Image:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. To assemble it, you bring the two flat sides together (the view is a "butterflied" version of the structure). On the left is the N-terminal part (roughly) with the nucleic acid forming a transcription bubble. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm. For an annotated image, see below.

[[Image:1msw legend.png|800px]]

<StructureSection load='' size='340' side='right' caption='' scene='10/1081719/T7_rnap/2'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/2'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>isosurface on; select protein; cartoon off; spacefill off</script>
<text>surface</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

User:Karsten Theis/T7RNAP physical model explanation

2025-06-20T02:41:12Z

Karsten Theis:

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[Image:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. To assemble it, you bring the two flat sides together (the view is a "butterflied" version of the structure). On the left is the N-terminal part (roughly) with the nucleic acid forming a transcription bubble. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm. For an annotated image, see below.

[[Image:1msw legend.png|800px]]

<StructureSection load='' size='340' side='right' caption='' scene='10/1081719/T7_rnap/1'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/2'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>isosurface on; select protein; cartoon off; spacefill off</script>
<text>surface</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

User:Karsten Theis/T7RNAP physical model explanation

2025-06-20T02:37:58Z

Karsten Theis:

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[Image:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. To assemble it, you bring the two flat sides together (the view is a "butterflied" version of the structure). On the left is the N-terminal part (roughly) with the nucleic acid forming a transcription bubble. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm. For an annotated image, see below.

[[Image:1msw legend.png|800px]]

<StructureSection load='' size='340' side='right' caption='' scene='10/1081719/T7_rnap/1'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/1'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>isosurface on; select protein; cartoon off; spacefill off</script>
<text>surface</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

Proteopedia:Cookbook

2025-06-02T19:58:30Z

Karsten Theis:

This page contains some advanced editing information. Make sure you looked at [[Help:Getting Started in Proteopedia]] and [[Help:Editing]] before you delve into this page.

==Text color==

'''{{Font color|red|Please}}
{{Font color|green|see}}'''
[[Help:Coloring text]].

==Tables==
Most of the tags to define a HTML table [https://www.w3schools.com/html/html_tables.asp] are valid in a Proteopedia wiki text.

The official [https://www.mediawiki.org/wiki/Help:Tables Help:Tables] warns "''Tables may be created in wiki pages. As a general rule, it is best to avoid using a table unless you need one. Table markup often complicates page editing''."

A good alternative is available at [https://www.tablesgenerator.com/mediawiki_tables tablesgenerator.com] with a good interface to generate tables that can be inserted in Proteopedia pages.

==Checkboxes, Buttons, Radio Buttons==
These can be used to toggle something in JSmol on/off, or for more complicated purposes, including running any JSmol script. See working examples at [[Proteopedia:DIY:Templates]], and more details in the [http://wiki.jmol.org/index.php/MediaWiki/ExtensionV4 Jmol Wiki].<br/>
Also see [[Jmol/Interactivity]].

==Font Awesome icons on pages <span class="fas fa-child"></span>==
You may choose from a large gallery of free [https://fontawesome.com/icons?d=gallery&m=free Font Awesome] icons .

The icon on the heading above was inserted with <b><nowiki><span class="fas fa-child"></span></nowiki></b>. Replace 'child' with the name of the icon you want to display. For those icons available on 'regular' and 'solid' modes, use either 'far' or 'fas' in the class.

Adding a CSS style allows to set color, size, background, etc. <b><nowiki><span class="far fa-lightbulb" style="color:#FF6600"></span></nowiki></b> <span class="far fa-lightbulb" style="color:#FF6600"></span>

==Jump to a specific green link==
To build a link (url2greenLink) to a specific <span style='color: green;'>green link</span> on a Proteopedia page, right click on the green link and Copy (not CopyLinkAddress). This will just copy the displayed text of the green link.

Add to the URL of the target page the sign '''#''' followed for the text you just copied, and press enter. This will force the browser to reformat the just created URL replacing spaces by %20 and encoding other special characters.

This is the url2greenLink you want.
Use this url2greenLink on a Proteopedia page as any other link to external sites: enclose the url2greenLink followed by space and the link text in single square brackets <nowiki>[url2greenLink one or more words]</nowiki>

This [http://proteopedia.org/w/Journal:PLoS_ONE:2#carboxylate%20group demo link] was created with the following text in this page
<pre>[http://proteopedia.org/w/Journal:PLoS_ONE:2#carboxylate%20group demo link]</pre>

'''Note:''' assign unique text to green links, to be able to address each one of the green links on a given page. Otherwise the jump will go to the first occurrence of the word(s).

==JSmol examples and documentation==
Tips, examples and advanced help for using JSmol are available at [https://wiki.jmol.org wiki.jmol.org], a complete Jmol/JSmol [https://chemapps.stolaf.edu/jmol/docs/ interactive script documentation] and
Jmol [https://chemapps.stolaf.edu/pe/protexpl/htm/seleccmd.htm select commands] with explanations.

==Translucent Cylinder==
[[Image:Translucent Cylinder 200px.gif|Translucent Cylinder]] Instructions and related examples at [[Jmol/Visualizing membrane position#Methods:_Translucent_Cylinder|Translucent Cylinder]]

==Side by side still images==
To arrange still images side by side on a page, insert them in a table
{|
| [[Image:1cjq.png|left|200px|]]
| [[Image:1stp.png|left|200px|]]
|}
<pre>
{|
| [[Image:1cjq.png|left|200px]]
| [[Image:1stp.png|left|200px]]
|}
</pre>
==Rectangular Jmol Structure Applets==
[http://jmol.sourceforge.net/jslibrary/ jslibrary] describes:<br>
For a rectangular Jmol structure applet, an array containing two elements, width and height; this is usually easiest to do using JavaScript square bracket notation for array constants, as in [400, 200], ["50%", "100%"] or [0.5, 1.0]. Proteopedia currently only accepts integers, as in this example <b>size='[800,200]'</b>

<Structure load='1stp' size='[400,100]' frame='true' align='left' caption='Insert caption here' />
{{Clear}}

==Synchronizing molecules==
Please see [[Jmol/Synchronization]]

==Capturing Movies==
On pages titled with a [[PDB ID]], simple rocking or spinning movies can be captured using the ''Export Animated Image'' link under the molecule, or by clicking ''FirstGlance'' in the Resources block, and then clicking ''Save Image or Animation for Powerpoint'' under the molecule (see
[http://firstglance.jmol.org/slides.htm overview]).

Complex operations and manual movements with the mouse can be captured as movies by "screen recording". Here are [http://firstglance.jmol.org/videocapture.htm examples and instructions].

==Movies mp4==
Click the ''Play'' icon below to start the sample movie.<br>
<html5media height="300" width="300" loop>/mp4/Resolution_holton.mp4</html5media>
{{Clear}}
<pre><html5media height="300" width="300" loop>/mp4/file.mp4</html5media></pre>
Shows the movie with the with a width of 300 and a height of 300 pixels. Including "loop" makes the movie loop back to the beginning while playing.

A movie controller is also displayed at the bottom beneath the movie. If the height is too small, the controller will not be displayed. Clicking on the movie stops playing, and clicking again resumes playing in both Mac OS X and Windows. This is
useful in case the controller is not displayed ("controller=false").

== Embedded Youtube ==
<html5media height="337" width="600">https://www.youtube.com/watch?v=Q1ftYq13XKk</html5media>

<pre><html5media height="337" width="600">https://www.youtube.com/watch?v=Q1ftYq13XKk</html5media></pre>

== Embedded Youtube Shorts ==
<html5media height="300" width="180">https://www.youtube.com/shorts/9hLJao96r0k</html5media>

The text that is visible upon starting the video goes away as you move your mouse out of the video window. It might be appropriate to mention that to the reader/viewer for better visibility.

==Embedded Vimeo ==
<html5media height="360" width="640">https://vimeo.com/235321305</html5media>

<pre><html5media height="360" width="640">https://vimeo.com/235321305</html5media></pre>

== Quiz ==
The special implementation of Quiz in Proteopedia includes an email feedback to the teacher.
See overview at [[Help:Quiz]] and the full explanation and examples on How To Use at [http://en.wikiversity.org/wiki/Help:Quiz Help:Quiz at Wikiversity].
<pre>
<quiz display=simple>
{
|type="{}"}
Name a famous Greek philosopher.
{ Aristotle|Plato }

{Question
|type="[]"}
+ Correct answer.
- Incorrect answer.
+ Correct answer.
- Incorrect answer.
</quiz>
</pre>

== Image as clickable link ==
People tend to click an image expecting it to take them to more about that image, via a hyperlink. Below is the wikitext to do this. This method goes to only one link target, regardless of where you click within the image. If you want to have different targets for different parts of the image, see the next section below on ''Imagemaps''.

<imagemap>
Image:Cys-spacefilled.png|100px
default [[Introduction to molecular visualization]]
</imagemap>
Clicking this image goes to ''Introduction to molecular visualization''.

<PRE>
<imagemap>
Image:Cys-spacefilled.png|100px
default [[Introduction to molecular visualization]]
</imagemap>
</PRE>

For more options, such as putting a border around the image, or aligning it to the right side of the page, please see [[Proteopedia:Image as clickable link]].

== Imagemaps ==

<big>In the image map below, clicking on the computer screen should lead you to '''2ace''', the keyboard to '''1rat''', <br>
and the ''thinking balloon'' to '''Believe It or Not!'''. A click on the person's head goes to the '''external article on Student at Wikipedia'''.<br>
The ''(i)'' goes to the image info.
</big>

<imagemap>
Image:Foo.jpg|200px|picture of a foo
poly 131 45 213 41 210 110 127 109 [[2ace]]
poly 104 126 105 171 269 162 267 124 [[1rat]]
rect 15 95 94 176 [http://en.wikipedia.org/wiki/Student]
# A comment, this line is ignored
circle 57 57 20 [[Believe_It_or_Not!]]
desc bottom-left
</imagemap>

<PRE>
<imagemap>
Image:Foo.jpg|200px|picture of a foo
poly 131 45 213 41 210 110 127 109 [[2ace]]
poly 104 126 105 171 269 162 267 124 [[1rat]]
rect 15 95 94 176 [http://en.wikipedia.org/wiki/Student]
# A comment, this line is ignored
circle 57 57 20 [[Believe_It_or_Not!]]
desc bottom-left
</imagemap>
</PRE>

[http://www.image-maps.com/ Here]'s a nice tool for finding the coordinates in an image.


==Structure Gallery Generator==
A list of PDB codes can generate small images and links automatically. See the [[Structure Gallery Generator]].

==Theoretical Models==
On pages that largely or entirely concern theoretical model structures, please insert '''<nowiki>{{Theoretical_model}}</nowiki>''' in the top of the wikitext box. It will generate this banner:
{{Theoretical_model}}

If a page shows largely empirical models, but also one or more theoretical models, please put <font color='red'>Theoretical Model</font> in the text, and/or as a caption in Jmol whenever the model is theoretical:
* The wikitext is: <nowiki>'''<font color='red'>Theoretical Model</font>'''</nowiki>
* To add the red caption to a scene, use the "labels" tab in the ''Scene Authoring Tools'' and open the "caption" section.

Policy concerning theoretical models is at [[Proteopedia:Policy#Theoretical_Models]], where you will also find links to '''examples'''.

==Anchors==
Section headings automatically act as anchors, with the heading text as the "anchor_name". Links of the form [[#anchor_name]] will link to the first anchor on the page matching that "anchor_name", usually the first identical section heading.

For example, try [[#Quiz]] ( <code><nowiki>[[#Quiz]]</nowiki></code> ) and [[#KiNG]] ( <code><nowiki>[[#KiNG]]</nowiki></code> ) to jump to those sections.

==Floating quote Box==
{{Quote box
| quote = Alice's Adventures in Wonderland by Lewis Carroll
| source = [http://www.gutenberg.org Project Gutemberg]
| width = 50%
| align = right
}}

There was nothing so very remarkable in that; nor did Alice think it so very much out of the way to hear the Rabbit say to itself, `Oh dear! Oh dear! I shall be late!' (when she thought it over afterwards, it occurred to her that she ought to have wondered at this, but at the time it all seemed quite natural); but when the Rabbit actually took a watch out of its waistcoat-pocket, and looked at it, and then hurried on, Alice started to her feet, for it flashed across her mind that she had never before seen a rabbit with either a waistcoat-pocket, or a watch to take out of it, and burning with curiosity, she ran across the field after it, and fortunately was just in time to see it pop down a large rabbit-hole under the hedge.

<PRE>
{{Quote box
| quote =
| source =
| width =
| align =
}}
</PRE>



==ConSurf==
To insert the ConSurf panel, type the following line

<noinclude><nowiki>{{subst:ConSurf|1stp|st}}</nowiki></noinclude>

where the 2 parameters, <b>1stp</b> and <b>st</b>, need to be adjusted to your case:
* First parameter is the PDB ID of the model.
* Second parameter is the 2nd and 3rd characters of the PDB ID.

The result will look like below and will be made a hard-coded content of the page (i.e. the template wikitext is removed and the result is inserted into the page source).


== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|right|200px]]
Check
<jmol>
<jmolCheckbox>
<scriptWhenChecked>
select protein; define ~consurf_to_do selected;
consurf_initial_scene = true;
script /wiki/ConSurf/st/1stp_consurf.spt;
</scriptWhenChecked>
<scriptWhenUnchecked>
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB].
You may read the [[Conservation%2C_Evolutionary|explanation]]
of the method and the full data available from
[http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1stp ConSurf].


==ConSurf Documentation==
[[ConSurf/Index]] has a list of many articles about ConSurf and evolutionary conservation.

==Combine Proteopedia scenes with JSmol scripting==

'''Advanced'''. You may wish to call up a scene saved via Proteopedia from within inline JSmol scripts placed in a page. For example, this can be useful for some pages that use multiple structures to call up a certain scene at the start of JSmol script be sure the user has the structure or scene open that you wish the inline JSmol script to build upon. Please see [[Combine Proteopedia scenes with inline JSmol scripting]].

==Mix and Edit scenes from other pages==
To load on SAT scenes from other Proteopedia pages and become able to edit them, simply insert the page ID (wgArticleId) of other pages between < > like this: '''''' somewhere in your page. You may insert this way as many page IDs as you want, and [[Scene_authoring_tools|SAT]] will allow you to load any scene from those pages. From that moment, any edited scene will be saved under your page, without altering the original scene nor the source page.
* How to find the page ID? Edit or view the source code (wikitext) of the page from which you want to borrow the scenes, find the <code>scene</code> tag and pick the number after the first slash, e.g. that in red here:
<scene name='58/<span style="color:red;">587840</span>/Cartoon_rainbow_and_water/1'>Color by group</scene>

==See Also==

* [[Proteopedia:DIY:Templates]]
* [[DRuMS#The DRuMS Color Schemes|DRuMS color templates]]
* [[Jmol/Interactivity]]

User:Karsten Theis/T7RNAP physical model explanation

2025-06-02T19:40:32Z

Karsten Theis:

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[Image:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. To assemble it, you bring the two flat sides together (the view is a "butterflied" version of the structure). On the left is the N-terminal part (roughly) with the nucleic acid forming a transcription bubble. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm. For an annotated image, see below.

[[Image:1msw legend.png|800px]]

<StructureSection load='' size='340' side='right' caption='' scene='10/1070504/T7_rnap/1'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/1'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>isosurface on; select protein; cartoon off; spacefill off</script>
<text>surface</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

User:Karsten Theis/T7RNAP physical model explanation

2025-06-02T19:39:11Z

Karsten Theis:

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[Image:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. To assemble it, you bring the two flat sides together (the view is a "butterflied" version of the structure). On the left is the N-terminal part (roughly) with the nucleic acid. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm. For an annotated image, see below.

[[Image:1msw legend.png|800px]]

<StructureSection load='' size='340' side='right' caption='' scene='10/1070504/T7_rnap/1'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/1'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>isosurface on; select protein; cartoon off; spacefill off</script>
<text>surface</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

File:1msw legend.png

2025-06-02T19:34:32Z

Karsten Theis:

== Licensing ==
{{self|cc-by-sa-3.0}}

Lipase lid morph

2025-06-02T18:56:32Z

Karsten Theis:

<Structure load='' size='400' frame='true' align='right' caption='Candida rugosa lipase ([[1trh]], [[1lpm]]).' scene='Lipase_lid_morph/Lightseagreen_hinge/1' />
For an introduction to the structure and function of lipase, please see the article [[Lipase]]. This ''Lipase lid morph'' article is a supplement to the main article on [[Lipase]].

''Candida rugosa'' lipase (triacylglycerol hydrolase) has been observed in two conformations, with the "lid" (residues 66-92<ref name='2states1994' />) closed ([[1trh]]) or open ([[1lpm]])<ref name='2states1994'>PMID: 8142901</ref>.

*Closed <font color='lightseagreen'><b>LID</b></font> (<scene name='Lipase_lid_morph/Lightseagreen_hinge/1'>restore initial scene</scene>).
*<scene name='Lipase_lid_morph/Lightseagreen_hinge/4'>Open</scene> <font color='lightseagreen'><b>LID</b></font> with inhibitor (1R)-menthyl hexyl phosphonate (<b><font color='#909090'>C</font> <font color='#ff0d0d'>O</font> <font color='#ff8000'>P</font></b>).

A morph<ref>This is a [[Morphs#Linear_Interpolation|linear interpolation morph]]. The 14-model PDB file is [[Image:Morph-linear-1trh-1lpm.pdb.gz]].</ref> shows the lid opening and closing.
*<scene name='Lipase_lid_morph/Lightseagreen_hinge/2'>Cartoon morph</scene> (<font color='lightseagreen'><b>LID</b></font>).
*<scene name='Lipase_lid_morph/Lightseagreen_hinge/3'>Spacefilling morph</scene> (<font color='lightseagreen'><b>LID</b></font>, <font color='orange'><b>catalytic triad: Ser209, Glu341, and His449</b></font><ref name='2states1994' />).<br>
{{Template:Button Toggle Animation2}}

When the lid is closed, the enzyme surface is largely {{Template:ColorKey_Polar}}. When the lid opens, a {{Template:ColorKey_Hydrophobic}} pocket is exposed with the catalytic triad in the bottom.

*<scene name='Lipase_lid_morph/Lightseagreen_hinge/5'>Spacefilling morph</scene> ({{Template:ColorKey_Polar}}, {{Template:ColorKey_Hydrophobic}}, <font color='orange'><b>catalytic triad: Ser209, Glu341, and His449</b></font><ref name='2states1994' />).

=== Rigid body morph ===

An <scene name='49/493694/Storymorph/1'>alternate morph</scene> shows a different path between the same initial and final experimental structures <ref>This is a rigid body morph based on the superposition in PDB file [[Image:1TRH_1LPM.pdb]]. It is created by the [[Jmol/Storymorph|Storymorph script]] on the fly.</ref>. The position of the inhibitor in the 1lpm structure is shown throughout; it would clash with the conformation of the lid in the 1trh structures, showing that closed lid and inhibitor binding are mutually exclusive.

<jmol>
<jmolButton>
<script>script "https://proteopedia.org/wiki/images/a/a2/Storymorph.spt";
domain2 = {(75-85)};
model 2;
structures = [{1.2}, {1.1}];
domains = [
[{protein and not domain2}],
[{domain2}, {(74,86) and *.CA}],
];
morph_palindrome = 1;
morph(15,structures,domains);</script>
<text>Run alternate morph</text>
</jmolButton>
</jmol>

==See Also==
*[[Lipase]], the main article in Proteopedia.
*[[Molecular Playground/Pancreatic Lipase]]
*[http://en.wikipedia.org/wiki/Lipase Lipase in Wikipedia]

==Notes and References==
<references />

User:Karsten Theis/T7RNAP physical model explanation

2025-06-02T18:55:42Z

Karsten Theis:

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[Image:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. On the left is the N-terminal part (roughly) with the nucleic acid. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm.

<StructureSection load='' size='340' side='right' caption='' scene='10/1070504/T7_rnap/1'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/1'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>isosurface on; select protein; cartoon off; spacefill off</script>
<text>surface</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

Proteopedia:Cookbook

2025-06-02T18:17:20Z

Karsten Theis:

This page contains some advanced editing information. Make sure you looked at [[Help:Getting Started in Proteopedia]] and [[Help:Editing]] before you delve into this page.

==Text color==

'''{{Font color|red|Please}}
{{Font color|green|see}}'''
[[Help:Coloring text]].

==Tables==
Most of the tags to define a HTML table [https://www.w3schools.com/html/html_tables.asp] are valid in a Proteopedia wiki text.

The official [https://www.mediawiki.org/wiki/Help:Tables Help:Tables] warns "''Tables may be created in wiki pages. As a general rule, it is best to avoid using a table unless you need one. Table markup often complicates page editing''."

A good alternative is available at [https://www.tablesgenerator.com/mediawiki_tables tablesgenerator.com] with a good interface to generate tables that can be inserted in Proteopedia pages.

==Checkboxes, Buttons, Radio Buttons==
These can be used to toggle something in JSmol on/off, or for more complicated purposes, including running any JSmol script. See working examples at [[Proteopedia:DIY:Templates]], and more details in the [http://wiki.jmol.org/index.php/MediaWiki/ExtensionV4 Jmol Wiki].<br/>
Also see [[Jmol/Interactivity]].

==Font Awesome icons on pages <span class="fas fa-child"></span>==
You may choose from a large gallery of free [https://fontawesome.com/icons?d=gallery&m=free Font Awesome] icons .

The icon on the heading above was inserted with <b><nowiki><span class="fas fa-child"></span></nowiki></b>. Replace 'child' with the name of the icon you want to display. For those icons available on 'regular' and 'solid' modes, use either 'far' or 'fas' in the class.

Adding a CSS style allows to set color, size, background, etc. <b><nowiki><span class="far fa-lightbulb" style="color:#FF6600"></span></nowiki></b> <span class="far fa-lightbulb" style="color:#FF6600"></span>

==Jump to a specific green link==
To build a link (url2greenLink) to a specific <span style='color: green;'>green link</span> on a Proteopedia page, right click on the green link and Copy (not CopyLinkAddress). This will just copy the displayed text of the green link.

Add to the URL of the target page the sign '''#''' followed for the text you just copied, and press enter. This will force the browser to reformat the just created URL replacing spaces by %20 and encoding other special characters.

This is the url2greenLink you want.
Use this url2greenLink on a Proteopedia page as any other link to external sites: enclose the url2greenLink followed by space and the link text in single square brackets <nowiki>[url2greenLink one or more words]</nowiki>

This [http://proteopedia.org/w/Journal:PLoS_ONE:2#carboxylate%20group demo link] was created with the following text in this page
<pre>[http://proteopedia.org/w/Journal:PLoS_ONE:2#carboxylate%20group demo link]</pre>

'''Note:''' assign unique text to green links, to be able to address each one of the green links on a given page. Otherwise the jump will go to the first occurrence of the word(s).

==JSmol examples and documentation==
Tips, examples and advanced help for using JSmol are available at [https://wiki.jmol.org wiki.jmol.org], a complete Jmol/JSmol [https://chemapps.stolaf.edu/jmol/docs/ interactive script documentation] and
Jmol [https://chemapps.stolaf.edu/pe/protexpl/htm/seleccmd.htm select commands] with explanations.

==Translucent Cylinder==
[[Image:Translucent Cylinder 200px.gif|Translucent Cylinder]] Instructions and related examples at [[Jmol/Visualizing membrane position#Methods:_Translucent_Cylinder|Translucent Cylinder]]

==Side by side still images==
To arrange still images side by side on a page, insert them in a table
{|
| [[Image:1cjq.png|left|200px|]]
| [[Image:1stp.png|left|200px|]]
|}
<pre>
{|
| [[Image:1cjq.png|left|200px]]
| [[Image:1stp.png|left|200px]]
|}
</pre>
==Rectangular Jmol Structure Applets==
[http://jmol.sourceforge.net/jslibrary/ jslibrary] describes:<br>
For a rectangular Jmol structure applet, an array containing two elements, width and height; this is usually easiest to do using JavaScript square bracket notation for array constants, as in [400, 200], ["50%", "100%"] or [0.5, 1.0]. Proteopedia currently only accepts integers, as in this example <b>size='[800,200]'</b>

<Structure load='1stp' size='[400,100]' frame='true' align='left' caption='Insert caption here' />
{{Clear}}

==Synchronizing molecules==
Please see [[Jmol/Synchronization]]

==Capturing Movies==
On pages titled with a [[PDB ID]], simple rocking or spinning movies can be captured using the ''Export Animated Image'' link under the molecule, or by clicking ''FirstGlance'' in the Resources block, and then clicking ''Save Image or Animation for Powerpoint'' under the molecule (see
[http://firstglance.jmol.org/slides.htm overview]).

Complex operations and manual movements with the mouse can be captured as movies by "screen recording". Here are [http://firstglance.jmol.org/videocapture.htm examples and instructions].

==Movies mp4==
Click the ''Play'' icon below to start the sample movie.<br>
<html5media height="300" width="300" loop>/mp4/Resolution_holton.mp4</html5media>
{{Clear}}
<pre><html5media height="300" width="300" loop>/mp4/file.mp4</html5media></pre>
Shows the movie with the with a width of 300 and a height of 300 pixels. Including "loop" makes the movie loop back to the beginning while playing.

A movie controller is also displayed at the bottom beneath the movie. If the height is too small, the controller will not be displayed. Clicking on the movie stops playing, and clicking again resumes playing in both Mac OS X and Windows. This is
useful in case the controller is not displayed ("controller=false").

== Embedded Youtube ==
<html5media height="337" width="600">https://www.youtube.com/watch?v=Q1ftYq13XKk</html5media>

<pre><html5media height="337" width="600">https://www.youtube.com/watch?v=Q1ftYq13XKk</html5media></pre>

== Embedded Youtube Shorts ==
<html5media height="300" width="300">https://www.youtube.com/shorts/9hLJao96r0k</html5media>

The text that is visible upon starting the video goes away as you move your mouse out of the video window. It might be appropriate to mention that to the reader/viewer for better visibility.

==Embedded Vimeo ==
<html5media height="360" width="640">https://vimeo.com/235321305</html5media>

<pre><html5media height="360" width="640">https://vimeo.com/235321305</html5media></pre>

== Quiz ==
The special implementation of Quiz in Proteopedia includes an email feedback to the teacher.
See overview at [[Help:Quiz]] and the full explanation and examples on How To Use at [http://en.wikiversity.org/wiki/Help:Quiz Help:Quiz at Wikiversity].
<pre>
<quiz display=simple>
{
|type="{}"}
Name a famous Greek philosopher.
{ Aristotle|Plato }

{Question
|type="[]"}
+ Correct answer.
- Incorrect answer.
+ Correct answer.
- Incorrect answer.
</quiz>
</pre>

== Image as clickable link ==
People tend to click an image expecting it to take them to more about that image, via a hyperlink. Below is the wikitext to do this. This method goes to only one link target, regardless of where you click within the image. If you want to have different targets for different parts of the image, see the next section below on ''Imagemaps''.

<imagemap>
Image:Cys-spacefilled.png|100px
default [[Introduction to molecular visualization]]
</imagemap>
Clicking this image goes to ''Introduction to molecular visualization''.

<PRE>
<imagemap>
Image:Cys-spacefilled.png|100px
default [[Introduction to molecular visualization]]
</imagemap>
</PRE>

For more options, such as putting a border around the image, or aligning it to the right side of the page, please see [[Proteopedia:Image as clickable link]].

== Imagemaps ==

<big>In the image map below, clicking on the computer screen should lead you to '''2ace''', the keyboard to '''1rat''', <br>
and the ''thinking balloon'' to '''Believe It or Not!'''. A click on the person's head goes to the '''external article on Student at Wikipedia'''.<br>
The ''(i)'' goes to the image info.
</big>

<imagemap>
Image:Foo.jpg|200px|picture of a foo
poly 131 45 213 41 210 110 127 109 [[2ace]]
poly 104 126 105 171 269 162 267 124 [[1rat]]
rect 15 95 94 176 [http://en.wikipedia.org/wiki/Student]
# A comment, this line is ignored
circle 57 57 20 [[Believe_It_or_Not!]]
desc bottom-left
</imagemap>

<PRE>
<imagemap>
Image:Foo.jpg|200px|picture of a foo
poly 131 45 213 41 210 110 127 109 [[2ace]]
poly 104 126 105 171 269 162 267 124 [[1rat]]
rect 15 95 94 176 [http://en.wikipedia.org/wiki/Student]
# A comment, this line is ignored
circle 57 57 20 [[Believe_It_or_Not!]]
desc bottom-left
</imagemap>
</PRE>

[http://www.image-maps.com/ Here]'s a nice tool for finding the coordinates in an image.


==Structure Gallery Generator==
A list of PDB codes can generate small images and links automatically. See the [[Structure Gallery Generator]].

==Theoretical Models==
On pages that largely or entirely concern theoretical model structures, please insert '''<nowiki>{{Theoretical_model}}</nowiki>''' in the top of the wikitext box. It will generate this banner:
{{Theoretical_model}}

If a page shows largely empirical models, but also one or more theoretical models, please put <font color='red'>Theoretical Model</font> in the text, and/or as a caption in Jmol whenever the model is theoretical:
* The wikitext is: <nowiki>'''<font color='red'>Theoretical Model</font>'''</nowiki>
* To add the red caption to a scene, use the "labels" tab in the ''Scene Authoring Tools'' and open the "caption" section.

Policy concerning theoretical models is at [[Proteopedia:Policy#Theoretical_Models]], where you will also find links to '''examples'''.

==Anchors==
Section headings automatically act as anchors, with the heading text as the "anchor_name". Links of the form [[#anchor_name]] will link to the first anchor on the page matching that "anchor_name", usually the first identical section heading.

For example, try [[#Quiz]] ( <code><nowiki>[[#Quiz]]</nowiki></code> ) and [[#KiNG]] ( <code><nowiki>[[#KiNG]]</nowiki></code> ) to jump to those sections.

==Floating quote Box==
{{Quote box
| quote = Alice's Adventures in Wonderland by Lewis Carroll
| source = [http://www.gutenberg.org Project Gutemberg]
| width = 50%
| align = right
}}

There was nothing so very remarkable in that; nor did Alice think it so very much out of the way to hear the Rabbit say to itself, `Oh dear! Oh dear! I shall be late!' (when she thought it over afterwards, it occurred to her that she ought to have wondered at this, but at the time it all seemed quite natural); but when the Rabbit actually took a watch out of its waistcoat-pocket, and looked at it, and then hurried on, Alice started to her feet, for it flashed across her mind that she had never before seen a rabbit with either a waistcoat-pocket, or a watch to take out of it, and burning with curiosity, she ran across the field after it, and fortunately was just in time to see it pop down a large rabbit-hole under the hedge.

<PRE>
{{Quote box
| quote =
| source =
| width =
| align =
}}
</PRE>



==ConSurf==
To insert the ConSurf panel, type the following line

<noinclude><nowiki>{{subst:ConSurf|1stp|st}}</nowiki></noinclude>

where the 2 parameters, <b>1stp</b> and <b>st</b>, need to be adjusted to your case:
* First parameter is the PDB ID of the model.
* Second parameter is the 2nd and 3rd characters of the PDB ID.

The result will look like below and will be made a hard-coded content of the page (i.e. the template wikitext is removed and the result is inserted into the page source).


== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|right|200px]]
Check
<jmol>
<jmolCheckbox>
<scriptWhenChecked>
select protein; define ~consurf_to_do selected;
consurf_initial_scene = true;
script /wiki/ConSurf/st/1stp_consurf.spt;
</scriptWhenChecked>
<scriptWhenUnchecked>
script /wiki/extensions/Proteopedia/spt/initialview01.spt;
</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB].
You may read the [[Conservation%2C_Evolutionary|explanation]]
of the method and the full data available from
[http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1stp ConSurf].


==ConSurf Documentation==
[[ConSurf/Index]] has a list of many articles about ConSurf and evolutionary conservation.

==Combine Proteopedia scenes with JSmol scripting==

'''Advanced'''. You may wish to call up a scene saved via Proteopedia from within inline JSmol scripts placed in a page. For example, this can be useful for some pages that use multiple structures to call up a certain scene at the start of JSmol script be sure the user has the structure or scene open that you wish the inline JSmol script to build upon. Please see [[Combine Proteopedia scenes with inline JSmol scripting]].

==Mix and Edit scenes from other pages==
To load on SAT scenes from other Proteopedia pages and become able to edit them, simply insert the page ID (wgArticleId) of other pages between < > like this: '''''' somewhere in your page. You may insert this way as many page IDs as you want, and [[Scene_authoring_tools|SAT]] will allow you to load any scene from those pages. From that moment, any edited scene will be saved under your page, without altering the original scene nor the source page.
* How to find the page ID? Edit or view the source code (wikitext) of the page from which you want to borrow the scenes, find the <code>scene</code> tag and pick the number after the first slash, e.g. that in red here:
<scene name='58/<span style="color:red;">587840</span>/Cartoon_rainbow_and_water/1'>Color by group</scene>

==See Also==

* [[Proteopedia:DIY:Templates]]
* [[DRuMS#The DRuMS Color Schemes|DRuMS color templates]]
* [[Jmol/Interactivity]]

File:1MSW butterfly.png

2025-06-02T16:57:17Z

Karsten Theis:

== Licensing ==
{{self|cc-by-sa-3.0}}

User:Karsten Theis/T7RNAP physical model explanation

2025-06-02T16:55:51Z

Karsten Theis: New page: This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID 1msw). 800px Above is a photograph of the two parts of the model. On the left is ...

This is a tour of a physical model of the T7 virus RNA polymerase (PDB ID [[1msw]]).
[[File:1MSW butterfly.png|800px]]

Above is a photograph of the two parts of the model. On the left is the N-terminal part (roughly) with the nucleic acid. On the right is the C-terminal part (roughly), in the shape of the right hand, with the active site at the palm.

<StructureSection load='' size='340' side='right' caption='' scene='10/1070504/T7_rnap/1'>

<html5media height="400" width="300">https://www.youtube.com/watch?v=q3GUgPdEBbU</html5media>

You can track the video in the interactive scene by clicking the timestamp buttons. (<scene name='10/1070504/T7_rnap/1'>initial scene</scene>)

<jmol>
<jmolButton>
<script>moveto 0.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>t=0</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 782 -558 279 143.88} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text> 7</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 320 -808 495 177.79} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>14</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 311 706 -636 140.67} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>22</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 788 408 -461 122.55} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
<text>30</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>moveto 1.0 { 976 -176 -124 114.98} 100.0 0.0 0.0 {-17.5975 -34.407000000000004 -2.4944999999999986} 59.686702486397 {0 0 0} 0 0 0 3.0 0.0 0.0;
</script>
<text>..0</text>
</jmolButton>
</jmol>

The video starts with a view of the N-terminal part of the protein. You can see the exiting template DNA (blue) on the right. As the model rotates, the active site comes into view. In red, you can see the most recently added nucleotide (about 10 seconds in). The active site is formed by the C-terminal part of the protein, which is shaped like a right hand. Access to the active site (the "palm" of the hand) is in between the "thumb" (in front about 7 sec in) and "the fingers" (in front about 14 sec in). At 22 s in, you have view on the helical axis of the upstream DNA. At about 30 s in, you can see the RNA exit channel. At 36 s, we are back to the start, and you can press "rewatch" on the YouTube window to take another turn.

Also, use the widgets below to change representations.

Protein shown as <jmol>
<jmolRadioGroup>
<item>
<script>isosurface on; select protein; cartoon off; spacefill off</script>
<text>surface</text>
<checked>true</checked>
</item>
<item>
<script>isosurface off; select protein; spacefill only</script>
<text>spacefill</text>
<checked>false</checked>
</item>
<item>
<script>isosurface off; select protein; cartoon only; select not (helix or strand); cartoon 0.3 </script>
<text>cartoon</text>
<checked>false</checked>
</item>
</jmolRadioGroup>
</jmol>

<jmol>
<jmolButton>
<script>select nucleic; cartoon only</script>
<text>DNA/RNA as cartoon</text>
</jmolButton>
</jmol>

</StructureSection>
== References ==
<references/>

Amylose

2025-05-29T16:02:21Z

Karsten Theis:

'''Amylose''' is a linear polymer of glucose that occurs in starch. It occurs in foods such as grains and potatoes, and it is a major source of energy (calories) in most diets. There are three major forms of crystalline amylose, A, B, and V, that differ in the three-dimensional structure. Amylose can also occur as amorphous structure, for example in starch or when cooked in water. Amylose is distinct from amylopectin, which is a branched polymer of glucose, and from [[cellulose]], which is a linear polymer of glucose that differs in stereochemistry from amylose. In the context of naturally occurring starch, parts of amylopectin form semi-crystalline layers resembling amylose A or B, while amylose itself occurs in the amorphous parts.

==Structure==
<StructureSection load='' size='340' side='right' scene='82/824003/Amylose_v/5'>
<scene name='82/824003/Amylose_a/3'>Amylose A</scene> and B occur as parallel double-helices of glucose chains, with 6 glucose units per turn. In contrast, amylose V shows single helices, as illustrated in the crystal structure of <scene name='82/824003/Amylose_v/6'>cyclodextrine 26</scene> (same structure shown as <scene name='82/824003/Amylose_v/5'>cartoon</scene>). A more irregular conformation of a cyclic amylose occurs is found in complex with a protein in the structure [[5jiw]]. In solution, amylose occurs as flexible hydrated single helices. These can bind to small molecules to form inclusion complexes such as the famous starch/iodine/iodide complex. Because of the difficulty in characterizing non-crystalline or semi-crystalline polymeric materials with complex chemical makeup (variation in chain length and location of branch points), the structure of starch and its components <ref>Perez, Serge & Bertoft, Eric. (2010). The molecular structures of starch components and their contribution to the architecture of starch granules: A comprehensive review. Starch ‐ Stärke. 62. 389 - 420. 10.1002/star.201000013.</ref> is less well characterized than that of proteins.

</StructureSection>

== References ==
<references/>

Amylose

2025-05-29T15:52:17Z

Karsten Theis:

'''Amylose''' is a linear polymer of glucose that occurs in starch. It occurs in foods such as grains and potatoes, and it is a major source of energy (calories) in most diets. There are three major forms of crystalline amylose, A, B, and V, that differ in the three-dimensional structure. Amylose can also occur as amorphous structure, for example in starch or when cooked in water. Amylose is distinct from amylopectin, which is a branched polymer of glucose, and from [[cellulose]], which is a linear polymer of glucose that differs in stereochemistry from amylose. In the context of naturally occurring starch, parts of amylopectin form semi-crystalline layers resembling amylose A or B, while amylose itself occurs in the amorphous parts.

==Structure==
<StructureSection load='' size='340' side='right' caption='Caption for this structure' scene='82/824003/Amylose_v/4'>
<scene name='82/824003/Amylose_a/3'>Amylose A</scene> and B occur as parallel double-helices of glucose chains, with 6 glucose units per turn. In contrast, amylose V shows single helices, as illustrated in the crystal structure of <scene name='82/824003/Amylose_v/2'>cyclodextrine 26</scene> (same structure shown as <scene name='82/824003/Amylose_v/3'>cartoon</scene>). A more irregular conformation of a cyclic amylose occurs is found in complex with a protein in the structure [[5jiw]]. In solution, amylose occurs as flexible hydrated single helices. These can bind to small molecules to form inclusion complexes such as the famous starch/iodine/iodide complex. Because of the difficulty in characterizing non-crystalline or semi-crystalline polymeric materials with complex chemical makeup (variation in chain length and location of branch points), the structure of starch and its components <ref>Perez, Serge & Bertoft, Eric. (2010). The molecular structures of starch components and their contribution to the architecture of starch granules: A comprehensive review. Starch ‐ Stärke. 62. 389 - 420. 10.1002/star.201000013.</ref> is less well characterized than that of proteins.

</StructureSection>

== References ==
<references/>

Amylose

2025-05-29T15:40:41Z

Karsten Theis:

'''Amylose''' is a linear polymer of glucose that occurs in starch. It occurs in foods such as grains and potatoes, and it is a major source of energy (calories) in most diets. There are three major forms of crystalline amylose, A, B, and V, that differ in the three-dimensional structure. Amylose can also occur as amorphous structure, for example in starch or when cooked in water. Amylose is distinct from amylopectin, which is a branched polymer of glucose, and from [[cellulose]], which is a linear polymer of glucose that differs in stereochemistry from amylose. In the context of naturally occurring starch, parts of amylopectin form semi-crystalline layers resembling amylose A or B, while amylose itself occurs in the amorphous parts.

==Structure==
<StructureSection load='' size='340' side='right' caption='Caption for this structure' scene='82/824003/Amylose_v/4'>
<scene name='82/824003/Amylose_a/3'>Amylose A</scene> and B occur as parallel double-helices of glucose chains, with 6 glucose units per turn. In contrast, <scene name='82/824003/Amylose_v/2'>amylose V</scene> occurs as a single helix as shown in the figure (same structure shown as <scene name='82/824003/Amylose_v/3'>cartoon</scene>). A more irregular conformation of a cyclic amylose occurs is found in complex with a protein in the structure [[5jiw]]. In solution, amylose occurs as flexible hydrated single helices. These can bind to small molecules to form inclusion complexes such as the famous starch/iodine/iodide complex. Because of the difficulty in characterizing non-crystalline or semi-crystalline polymeric materials with complex chemical makeup (variation in chain length and location of branch points), the structure of starch and its components <ref>Perez, Serge & Bertoft, Eric. (2010). The molecular structures of starch components and their contribution to the architecture of starch granules: A comprehensive review. Starch ‐ Stärke. 62. 389 - 420. 10.1002/star.201000013.</ref> is less well characterized than that of proteins.

</StructureSection>

== References ==
<references/>

Amylose

2025-05-29T15:38:52Z

Karsten Theis:

'''Amylose''' is a linear polymer of glucose that occurs in starch. It occurs in foods such as grains and potatoes, and it is a major source of energy (calories) in most diets. There are three major forms of crystalline amylose, A, B, and V, that differ in the three-dimensional structure. Amylose can also occur as amorphous structure, for example in starch or when cooked in water. Amylose is distinct from amylopectin, which is a branched polymer of glucose, and from [[cellulose]], which is a linear polymer of glucose that differs in stereochemistry from amylose. In the context of naturally occurring starch, parts of amylopectin form semi-crystalline layers resembling amylose A or B, while amylose itself occurs in the amorphous parts.

==Structure==
<StructureSection load='' size='340' side='right' caption='Caption for this structure' scene='82/824003/Amylose_v/4'>
<scene name='82/824003/Amylose_a/3'>Amylose A</scene> and B occur as parallel double-helices of glucose chains, with 6 glucose units per turn. In contrast, <scene name='82/824003/Amylose_v/2'>amylose V</scene> occurs as a single helix as shown in the figure (same structure shown as <scene name='82/824003/Amylose_v/3'>cartoon</scene>). A more irregular conformation of a cyclic amylose occurs is found in complex with a protein in the structure [[5jiw]]. In solution, amylose occurs as flexible hydrated single helices. These can bind to small molecules to form inclusion complexes such as the famous starch/iodine/iodide complex. Because of the difficulty in characterizing non-crystalline or semi-crystalline polymeric materials with complex chemical makeup (variation in chain length and location of branch points), the structure of starch and its components <ref>DOI:10.1002/star.201000013</ref> is less well characterized than that of proteins.

</StructureSection>

== References ==
<references/>

Amylose

2025-05-29T14:55:27Z

Karsten Theis:

'''Amylose''' is a linear polymer of glucose that occurs in starch. It occurs in foods such as grains and potatoes, and it is a major source of energy (calories) in most diets. There are three major forms of crystalline amylose, A, B, and V, that differ in the three-dimensional structure. Amylose can also occur with an undefined structure, for example when cooked in water. Amylose is distinct from amylopectin, which is a branched polymer of glucose, and from [[cellulose]], which is a linear polymer of glucose that differs in stereochemistry from amylose. In the context of naturally occurring starch, parts of amylopectin form semi-crystalline layers resembling amylose A or B, while amylose itself occurs in the amorphous parts.

==Structure==
<StructureSection load='' size='340' side='right' caption='Caption for this structure' scene='82/824003/Amylose_v/4'>
<scene name='82/824003/Amylose_a/3'>Amylose A</scene> and B occur as parallel double-helices of glucose chains, with 6 glucose units per turn. In contrast, <scene name='82/824003/Amylose_v/2'>amylose V</scene> occurs as a single helix as shown in the figure (same structure shown as <scene name='82/824003/Amylose_v/3'>cartoon</scene>). A more irregular conformation of a cyclic amylose occurs is found in complex with a protein in the structure [[5jiw]]. In solution, amylose occurs as flexible hydrated single helices. These can bind to small molecules to form inclusion complexes such as the famous starch/iodine/iodide complex. Because of the difficulty in characterizing non-crystalline or semi-crystalline polymeric materials with complex chemical makeup (variation in chain length and location of branch points), the structure of starch and its components <ref>DOI:10.1002/star.201000013</ref> is less well characterized than that of proteins.

</StructureSection>

== References ==
<references/>

Amylose

2025-05-29T14:53:59Z

Karsten Theis:

'''Amylose''' is a linear polymer of glucose that occurs in starch. It occurs in foods such as grains and potatoes, and it is a major source of energy (calories) in most diets. There are three major forms of crystalline amylose, A, B, and V, that differ in the three-dimensional structure. Amylose can also occur with an undefined structure, for example when cooked in water. Amylose is distinct from amylopectin, which is a branched polymer of glucose, and from [[cellulose]], which is a linear polymer of glucose that differs in stereochemistry from amylose. In the context of naturally occurring starch, parts of amylopectin form semi-crystalline layers, while amylose occurs in the amorphous parts.

==Structure==
<StructureSection load='' size='340' side='right' caption='Caption for this structure' scene='82/824003/Amylose_v/4'>
<scene name='82/824003/Amylose_a/3'>Amylose A</scene> and B occur as parallel double-helices of glucose chains, with 6 glucose units per turn. In contrast, <scene name='82/824003/Amylose_v/2'>amylose V</scene> occurs as a single helix as shown in the figure (same structure shown as <scene name='82/824003/Amylose_v/3'>cartoon</scene>). A more irregular conformation of a cyclic amylose occurs is found in complex with a protein in the structure [[5jiw]]. In solution, amylose occurs as flexible hydrated single helices. These can bind to small molecules to form inclusion complexes such as the famous starch/iodine/iodide complex. Because of the difficulty in characterizing non-crystalline or semi-crystalline polymeric materials with complex chemical makeup (variation in chain length and location of branch points), the structure of starch and its components <ref>DOI:10.1002/star.201000013</ref> is less well characterized than that of proteins.

</StructureSection>

== References ==
<references/>

User:Karsten Theis/Molecular Playground

2025-05-28T13:27:45Z

Karsten Theis:

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

<html5media height="337" width="600">https://www.youtube.com/watch?v=gzlKHNoZdYc</html5media>

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

What should you check before you save an existing scene?

# Make sure the parts of interest stay in view as you rotate the molecule
# Decide whether your background should be black (works well) or something else
# Choose a descriptive file name

What are the advantages of creating and loading a pngj file?

# It contains everything Jmol needs for the initial scene, including the coordinates
# It preserves the orientation
# It has a built-in preview that works without Jmol

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], normal modes in crystals [https://www.crystal.unito.it/animations_vibrational_modes.html], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console). Complex visualizations might be slower here than on molecular playground because the Jmol application is more powerful than the applet used in the browser.

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[1024,693]' frame='true' align='right' caption='' scene='' />

<jmol>
<jmolLink>
<script> script /images/5/5e/Benzene_cyclohexane.spt
</script>
<text>Cyclohexane vs Benzene</text>
</jmolLink>
</jmol>

<jmol>
<jmolLink>
<script> script /images/c/c6/Cellulose.spt
</script>
<text>Cellulose</text>
</jmolLink>
</jmol>

File:Uvrb fancy.spt

2025-05-21T02:02:23Z

Karsten Theis: uploaded a new version of "Image:Uvrb fancy.spt"

== Summary ==
Testing a concept of selecting the next scene by rotation
== Licensing ==
{{self|cc-by-sa-3.0}}

User:Karsten Theis/Sandbox 2

2025-05-21T01:57:50Z

Karsten Theis:

File:Uvrb fancy.spt

2025-05-21T01:57:11Z

Karsten Theis: Testing a concept of selecting the next scene by rotation

== Summary ==
Testing a concept of selecting the next scene by rotation
== Licensing ==
{{self|cc-by-sa-3.0}}

User:Karsten Theis/Sandbox 2

2025-05-21T01:53:10Z

Karsten Theis:

<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/5/5e/Benzene_cyclohexane.spt
</script>
<text>Cyclohexane vs Benzene</text>
</jmolLink>
</jmol>

<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt
</script>
<text>UvrB single scene</text>
</jmolLink>
</jmol>

<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt
function selector(selections) {
x_min = 0.4 * _width
x_max = 0.6 * _width
y_min = 0.4 * _height
y_max = 0.6 * _height
focus = {clickable and (sy > y_min and sy < y_max and sx > x_min and sx < x_max)}
minz = 0
best = 0
for (var j FROM [1,selections.length]) {
a = selections[j] and focus
if (a.length > 0) {
if ((best = 0) or (minz > a.sz)) {
best = j
minz = a.sz
}
}
}
return best
}

selections = [{ATP}, {91-117}, {157-245}]
old_s = 0
times = 0
while (times < 2) {
delay 2
s = selector(selections)
print s
if (s > 0) {
select @{selections[s]}
selectionhalos on
delay 5
}
if (s = old_s) {
selectionhalos off
hide not selected
select none
center visible
times = times + 1
delay 10
hide none
select none
center visible
zoom 100
delay 5
s = 0
}
old_s = s
}
print "script done"
</script>
<text>UvrB selector test</text>
</jmolLink>
</jmol>

<jmol>
<jmolLink>
<script> script /images/c/c8/UvrB_tour.spt
</script>
<text>UvrB tour</text>
</jmolLink>
</jmol>

User:Karsten Theis/Trypsin

2025-05-15T15:44:55Z

Karsten Theis:

This is a lesson on Trypsin, a serine protease. It assumes you already know how chymotrypsin, another serine protease, works. It explores substrate specificity, activation and degradation, and relationship to thrombin.

By the end of this brief session, students will be able to:

* Explain how substrate specificity in trypsin is achieved, emphasizing the role of Asp189 in recognizing and binding positively charged residues like Arg and Lys.

* Compare the substrate-binding pockets of trypsin and chymotrypsin, noting how differences in residue composition drive specificity.

* Describe the biological importance of regulating trypsin activation and degradation, considering the fact that a significant portion of amino acids in the gut come from digestive enzymes themselves.

* Recognize the historical and structural relevance of trypsin as a model for thrombin, and appreciate how this influenced early biochemical and structural studies.

Center on:
<jmol>
<jmolButton>
<script>center HIS and 57</script>
<text>His 57</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>center SER and 195</script>
<text>Ser 195</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>center ASP and 189</script>
<text>Asp 189</text>
</jmolButton>
</jmol>
==Figures==
<StructureSection load='' size='550' side='right' caption='' scene='10/1071246/Trypsin_5mop/5'>

Figure 1: <scene name='10/1071246/Trypsin_5mop/4'>overall view</scene>

Transition: <scene name='10/1071246/Overall_1oph/1'>overall view in 1oph</scene>

Figure 2: <scene name='10/1071246/Pocket/3'>P1 pocket</scene>
with <scene name='10/1071246/Pocket/4'>mesh</scene>

Figure 3: with <scene name='10/1071246/Pocket/4'>mesh</scene>

Figure 4: <scene name='10/1071246/Trypsinogen_2tgt_trypsin_2ptn/2'>Trypsinogen superposition</scene>

<jmol>
<jmolButton>
<script>!exit; ppdiaCaptionCmd = "changeCaption('Trypsin binds to its N-terminus, loops are ordered, and it is active','white','black');"; javascript @ppdiaCaptionCmd; model 1</script>
<text>active</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>!exit; ppdiaCaptionCmd = "changeCaption('Trypsinogen has disordered loops, including its (longer) N-terminus','white','black');";
javascript @ppdiaCaptionCmd;model 2</script>
<text>inactive</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>!exit; ppdiaCaptionCmd = "changeCaption('Superposition of trypsin(green) and trypsinogen(maroon)','white','black');"; javascript @ppdiaCaptionCmd; model 0</script>
<text>both</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>animation mode loop; ppdiaCaptionCmd = "changeCaption('Animated superposition of trypsin(green) and trypsinogen(maroon).','white','black');"; javascript @ppdiaCaptionCmd; animation on</script>
<text>animate</text>
</jmolButton>
</jmol>

Figure 5: inhibitor complex

<ref>PMID:6207021</ref>

<ref>PMID: 10181</ref>

== Further reading ==

https://www.worthington-biochem.com/products/trypsin/manual (alpha trypsin, beta, anionic, cationic...)

anhydro: treated to convert serines to anhydroalanines

https://www.elegantexperiments.net/en/post/length-digestive-system/ digestive tract length

https://derangedphysiology.com/main/cicm-primary-exam/gastrointestinal-system/Chapter-110/composition-volumes-and-regulation-gastrointestinal-secretions volume of secretions

https://pubmed.ncbi.nlm.nih.gov/24694282/ Surface area (tennis court or badminton court?)

== References ==

<references/>

</StructureSection>

User:Karsten Theis/Trypsin

2025-05-15T15:08:41Z

Karsten Theis:

Center on:
<jmol>
<jmolButton>
<script>center HIS and 57</script>
<text>His 57</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>center SER and 195</script>
<text>Ser 195</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>center ASP and 189</script>
<text>Asp 189</text>
</jmolButton>
</jmol>
==Figures==
<StructureSection load='' size='550' side='right' caption='' scene='10/1071246/Trypsin_5mop/5'>

Figure 1: <scene name='10/1071246/Trypsin_5mop/4'>overall view</scene>

Transition: <scene name='10/1071246/Overall_1oph/1'>overall view in 1oph</scene>

Figure 2: <scene name='10/1071246/Pocket/3'>P1 pocket</scene>
with <scene name='10/1071246/Pocket/4'>mesh</scene>

Figure 3: with <scene name='10/1071246/Pocket/4'>mesh</scene>

Figure 4: <scene name='10/1071246/Trypsinogen_2tgt_trypsin_2ptn/2'>Trypsinogen superposition</scene>

<jmol>
<jmolButton>
<script>!exit; ppdiaCaptionCmd = "changeCaption('Trypsin binds to its N-terminus, loops are ordered, and it is active','white','black');"; javascript @ppdiaCaptionCmd; model 1</script>
<text>active</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>!exit; ppdiaCaptionCmd = "changeCaption('Trypsinogen has disordered loops, including its (longer) N-terminus','white','black');";
javascript @ppdiaCaptionCmd;model 2</script>
<text>inactive</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>!exit; ppdiaCaptionCmd = "changeCaption('Superposition of trypsin(green) and trypsinogen(maroon)','white','black');"; javascript @ppdiaCaptionCmd; model 0</script>
<text>both</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>animation mode loop; ppdiaCaptionCmd = "changeCaption('Animated superposition of trypsin(green) and trypsinogen(maroon).','white','black');"; javascript @ppdiaCaptionCmd; animation on</script>
<text>animate</text>
</jmolButton>
</jmol>

Figure 5: inhibitor complex

<ref>PMID:6207021</ref>

<ref>PMID: 10181</ref>

== Further reading ==

https://www.worthington-biochem.com/products/trypsin/manual (alpha trypsin, beta, anionic, cationic...)

anhydro: treated to convert serines to anhydroalanines

https://www.elegantexperiments.net/en/post/length-digestive-system/ digestive tract length

https://derangedphysiology.com/main/cicm-primary-exam/gastrointestinal-system/Chapter-110/composition-volumes-and-regulation-gastrointestinal-secretions volume of secretions

https://pubmed.ncbi.nlm.nih.gov/24694282/ Surface area (tennis court or badminton court?)

== References ==

<references/>

</StructureSection>

File:Molecular playground helpers.spt

2025-05-09T16:00:02Z

Karsten Theis: uploaded a new version of "Image:Molecular playground helpers.spt"

== Summary ==
Helper functions to show molecular playground scenes in applet (online) or app (offline).
== Licensing ==
{{self|cc-by-sa-3.0}}

Lesson: beta turns

2025-05-09T15:26:58Z

Karsten Theis:

A '''beta turn''' is a secondary structure element consisting of four consecutive amino acids (or three consecutive peptide planes). The geometry of turns correspond to a change in the direction of the polypeptide backbone, with a short distance between the first and fourth alpha carbon.

==Concepts you can explore here==

# A beta turn is a secondary structure element distinct from (but sometimes overlapping with) alpha helices and beta strands
# Beta turns consist of stretches of four amino acids making a sharp turn, with a short distance between the first and last alpha carbon
# Beta turns typically occur near the surface of globular proteins, often connecting helices and strands
# There are multiple types of beta turns, distinguished by the torsion angles of the second and third residue
# Glycine and proline occur relatively often in beta turns and play distinct special roles

See the [[Talk:Lesson:_beta_turns|discussion tab]] for learning and teaching notes.

==Turns in 3D==

<StructureSection load='' size='350' side='right' caption='' scene='10/1072233/Turn_2mhr/2'>
===Basic features===
The interactive Jmol window on the right shows a beta turn (<scene name='10/1072233/Turn_2mhr/2'>reload initial scene</scene>) indicating the short distance between the first and the fourth alpha carbon. Because of this short distance, the polypeptide takes a sharp turn, sometimes also called a reverse turn. There are many types of beta turns, and they differ in the [[Tutorial:Ramachandran_principle_and_phi_psi_angles|phi and psi angles]] of residues two and three<ref>PMID:7756980</ref>. Some turns feature a <scene name='10/1072233/Turn_2mhr/4'>hydrogen bond</scene> between residues one and four (like the one shown here) and others don't.

===Beta turns in the context of other secondary structures===
The repetitive secondary structure elements ([[Alpha helix|alpha helices]] and [[Sheets in Proteins|beta strands]]) go in a single direction. Turns change the direction of the main chain, allowing them to connect alpha helices and beta strands at the surface of a globular protein. Of the six main chain hydrogen bonding partners of a turn, a maximum of two are engaged in hydrogen bonding, and turns are rarely found in the hydrophobic core. Below are three different protein folds highlighting the role of turns and their positions within a fold.

====Turns in an all-alpha protein====

In this <scene name='10/1072233/Alpha_2hmr/4'>myohemerythrin</scene> protein, you can see beta turns connecting the anti-parallel alpha helices. You can <jmol><jmolLink>
<script>
view1 = script("show moveto")[11][0];
select (67-70 and mainchain) or (68-69 and *.CB);
moveto 0.5 { 396 918 -22 24.97} 132.25 0.0 0.0 {27.01119230769231 33.81188461538462 10.03376923076923} 43.963541342342076 {0 0 0} 0 0 0 3.0 0.0 0.0;
wireframe 0.3;
color cpk;
select 67-70;
backbone off;
delay 0.5;
moveto 1.0 { 455 178 -872 110.43} 935.76 0.0 0.0 {26.793 33.036 8.6745} 44.96343106192573 {0 0 0} 0 0 0 3.0 0.0 0.0;
slab on
slab 60
delay 6;
select 67-70; backbone 0.4; wireframe off;
slab off;
script inline @{"moveto 1.0" + view1};
</script>
<text>zoom in</text>
</jmolLink>
</jmol> on the turn shown in the initial scene (and used below to explore conformations).

====Turns in an all-beta protein====
In this <scene name='10/1072233/Agglutinin/3'>agglutinin protein</scene>, you can see beta turns connecting the strands of anti-parallel beta sheets. Two antiparallel beta strands directly connected by a turn is called a <jmol><jmolLink>
<script>spin off; moveto 1.0 { 788 -362 -499 99.91} 404.55 0.0 0.0 {48.10615151515151 42.74112121212122 9.030939393939395} 37.460536158500446 {0 0 0} 0 0 0 3.0 0.0 0.0; delay 0.5; set zshade on; select protein; backbone -0.5;
</script>
<text>beta hairpin structure</text>
</jmolLink>
</jmol>. In this case, residues 1 and 4 of the turn are also part of the strands. This overlap of secondary structure assignment is common, but residues 2 and 3 of the turn are never part of a strand or an helix, by definition.

====Turns in an alpha/beta protein====

In this <scene name='10/1072233/Tim/3'>TIM barrel protein</scene>, you can see beta turns connecting helices and strands. The beta sheet is a barrel of parallel strands, as you can see if you turn on the cartoon representation with the buttons below.

The buttons below alow you to change the background color, spin the molecule, change the style and turn on the Ramachandran plot for 10 seconds.
<jmol>
<jmolButton>
<script>background white</script>
<text>white</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>background black</script>
<text>black</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>spin y -50</script>
<text>fastspin</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>spin off</script>
<text>spin off</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>select protein; cartoon on; backbone off</script>
<text>cartoon</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>select protein; backbone 0.5; cartoon off</script>
<text>trace</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>set zshade on; set zshadepower 2</script>
<text>zshade</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>save state ~one;
plot ramachandran; delay 10; restore state ~one</script>
<text>rama</text>
</jmolButton>
</jmol>

===Exploring torsion angles of turns===

The interactive Jmol window shows a <scene name='10/1072233/Turn_2mhr/1'>turn</scene> (residues 67-70 of the [[2hmr]] structure shown previously) that you can explore. Four consecutive amino acids are said to form a beta turn if the alpha carbon atoms of the first and the fourth residue are in close proximity (less than 7.0 or 7.5 Angstrom<ref>PMID:36293166</ref>). However, this also happens in alpha helices and 3(10) helices, and these are not classified as beta turn.

In the structure fragment shown, the alpha carbon atoms are numbered 1 through 4 (relative numbering, sometimes also given as n, n+1, n+2, n+3), and the distance between the carbonyl oxygen and the amide hydrogen is indicated (dashed line and magnitude). Side chains are truncated to just show the beta carbon, and residues 1 and 4 have some main chain omitted for clarity.

Another way of looking at it is that turns consist of three <jmol><jmolLink>
<script>
draw ID p68a polygon [{68.CA} {69.H} {69.CA}] color blue;
draw ID p68b polygon [{68.CA} {69.CA} {68.O}] color red;
draw ID p67a polygon [{67.CA} {68.H} {68.CA}] color blue;
draw ID p67b polygon [{67.CA} {68.CA} {67.O}] color red;
draw ID p69a polygon [{69.CA} {70.H} {70.CA}] color blue;
draw ID p69b polygon [{69.CA} {70.CA} {69.O}] color red;
delay 2; hide protein; delay 5; display protein; delay 1; draw ID p* delete;
</script>
<text>peptide planes</text>
</jmolLink>
</jmol>, whose relative orientation is determined by the phi/psi angles of residue 2 and 3.

The buttons below allow you to modify the conformation of the turn by changing the relevant torsion angles. To get a low energy conformation, you want a good hydrogen bond, i.e. carbonyl oxygen, amide hydrogen and nitrogen colinear <jmol>
<jmolLink>
<script>
define current selected;
select 67.O or 70.N or 70.H;
spacefill 30%;
selectionHalos on;
delay 1.5;
selectionHalos off;
spacefill off
select current;
</script>
<text>(☼)</text>
</jmolLink>
</jmol>, and want to avoid any clashes, e.g. carbonyl oxygen <jmol>
<jmolLink>
<script>
define current selected;
select *.O and visible;
spacefill 30%;
selectionHalos on;
delay 1.5;
selectionHalos off;
spacefill off
select current;
</script>
<text>(☼)</text>
</jmolLink>
</jmol> too close to beta carbon <jmol>
<jmolLink>
<script>
define current selected;
select *.CB and visible;
spacefill 30%;
selectionHalos on;
delay 1.5;
selectionHalos off;
spacefill off;
select current;
</script>
<text>(☼)</text>
</jmolLink>
</jmol> of the side chains.

====Excercise 1====

Turns have been classified into different types in different ways, but most classifications include type I, type II, and type I' <ref>PMID: 3184187</ref>. Try to use the buttons to make a type I turn with the features shown below. This is the most common beta turn (more than one third are of this type). Are there any clashes? How is the different from an alpha helix (where all carbonyl groups are pointing in the same direction)?

Before you start, make sure a single turn is displayed in the Jmol window on the right (<scene name='10/1072233/Turn_2mhr/1'>reload</scene>).

Phi&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {68.CA} {68.N} 10</script>
<text>+</text>
</jmolButton>
</jmol> 2 <jmol>
<jmolButton>
<script>rotate BRANCH {68.CA} {68.N} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {69.N}{69.CA} 10</script>
<text>+</text>
</jmolButton>
</jmol> 3 <jmol>
<jmolButton>
<script>rotate BRANCH {69.N}{69.CA} -10</script>
<text>−</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>save state ~one;
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
<text>Ramachandran</text>
</jmolButton>
</jmol>
Psi&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {68.C}{68.CA} 10</script>
<text>+</text>
</jmolButton>
</jmol> 2 <jmol>
<jmolButton>
<script>rotate BRANCH {68.C}{68.CA} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {69.CA}{69.C} 10</script>
<text>+</text>
</jmolButton>
</jmol> 3 <jmol>
<jmolButton>
<script>rotate BRANCH {69.CA}{69.C} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;&emsp;<jmol>
<jmolButton>
<script>original = {all}.xyz.all;rotate BRANCH {68.CA}{68.C} 180;rotate BRANCH {69.N}{69.CA} 180;rotate COMPARE {all} @original
</script>
<text>pepflip</text>
</jmolButton>
</jmol>

[[Image:Beta_turn_type_I.png|500px]]

====Excercise 2====

And now try to get a type I prime conformation, as shown below. This turn is rare (about 4% of beta turns are of this type). Hint: the pepflip button might serve as a bit of a shortcut. Why is that? Are there any clashes? If you had to choose, would you place a glycine at position 2 or position 3?

[[Image:Beta_turn_type_I_prime.png|500px]]

Before you start, make sure a single turn is displayed in the Jmol window on the right (<scene name='10/1072233/Turn_2mhr/3'>reload</scene>).

Phi&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {68.CA} {68.N} 10</script>
<text>+</text>
</jmolButton>
</jmol> 2 <jmol>
<jmolButton>
<script>rotate BRANCH {68.CA} {68.N} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {69.N}{69.CA} 10</script>
<text>+</text>
</jmolButton>
</jmol> 3 <jmol>
<jmolButton>
<script>rotate BRANCH {69.N}{69.CA} -10</script>
<text>−</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>save state ~one;
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
<text>Ramachandran</text>
</jmolButton>
</jmol>

Psi&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {68.C}{68.CA} 10;
</script>
<text>+</text>
</jmolButton>
</jmol> 2 <jmol>
<jmolButton>
<script>rotate BRANCH {68.C}{68.CA} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {69.CA}{69.C} 10</script>
<text>+</text>
</jmolButton>
</jmol> 3 <jmol>
<jmolButton>
<script>rotate BRANCH {69.CA}{69.C} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;&emsp;<jmol>
<jmolButton>
<script>original = {all}.xyz.all;rotate BRANCH {68.CA}{68.C} 180;rotate BRANCH {69.N}{69.CA} 180;rotate COMPARE {all} @original
</script>
<text>pepflip</text>
</jmolButton>
</jmol>

====Exercise 3====
Compare and contrast the two turns we discussed, and compare them to alpha helix and beta sheet. Clicking the buttons will preserve the orientation of the 2->3 peptide plane <jmol>
<jmolLink>
<script>
define current selected;
select 68.C or 68.O or 69.N or 69.H;
spacefill 30%;
select 68.CA or 68.C or 68.O or 69.N or 69.H or 69.CA;
selectionHalos on;
delay 0.8;
selectionHalos off;
select 68.C or 68.O or 69.N or 69.H;
spacefill off;
select current;
</script>
<text>(☼)</text>
</jmolLink>
</jmol> while adjusting the torsion angles. You can press the last button to rotate the entire molecules as a rigid body (different from the pepflip button above, which changes torsion angles).

Before you start, make sure a single turn is displayed in the Jmol window on the right (<scene name='10/1072233/Turn_2mhr/3'>reload</scene>).

<jmol>
<jmolButton>
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;
rpsi2 = -30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA} @rpsi2;
rphi3 = -90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;
rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3;
set echo top center; echo "Type I"; color echo white</script>
<text>Type I</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -57 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -47 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -57 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -47 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "alpha helix"</script>
<text>(alpha helix)</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -49 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -26 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -49 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -26 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "3-10 helix"</script>
<text>(3-10 helix)</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -140 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 130 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -140 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 130 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "beta strand"</script>
<text>(beta strand)</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = 60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type I prime"</script>
<text>Type I prime</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 120 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 80 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type II"</script>
<text>Type II</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -120 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 120 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type VIII"</script>
<text>Type VIII</text>
</jmolButton>
</jmol>

<jmol>
<jmolButton>
<script>rotate X 180 180</script>
<text>rotate along x-axis</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>center visible</script>
<text>center</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>save state ~one;
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
<text>rama</text>
</jmolButton>
</jmol>

Here are some possible things to discuss: the orientation of the carbonyl groups, hydrogen bonding patterns, potential clashes of side chains with the main chain secondary structure conformation, regions of the Ramachandran plot, distance of certain pairs of atoms, cis and trans peptides (what?).

===Role of glycine and proline===

Glycine is the only amino acid lacking a side chain, allowing for a larger range of favorable phi/psi combinations. Proline, on the other hand, has a severely restricted range of phi torsion angles because it forms a five-membered ring involving the side chain and the main chain nitrogen. This allows these two amino acids to fulfil special roles in beta turns.

We will look at two examples from myohemethryin. The first shows a type II turn with <jmol>
<jmolLink>
<script>source /scripts/10/1072233/Alpha_2hmr/1.spt; background black; set zshade on; delay 0.5; moveto 1.0 { 68 -995 72 143.7} 132.25 0.0 0.0 {17.7825 49.4315 12.7155} 29.587605862640846 {0 0 0} 0 0 0 3.0 0.0 0.0;;
moveto 2.0 { 732 -555 394 175.75} 615.28 0.0 0.0 {15.7575 32.677 14.6085} 44.38762035414952 {0 0 0} 0 0 0 3.0 0.0 0.0;
source /scripts/10/1072233/Alpha_2hmr/2.spt; background black; set zshade on;delay 0.5;draw * off
</script>
<text>glycine in position 3</text>
</jmolLink>
</jmol>. A side chain in position 3 would clash with the carbonyl group of the central peptide plane of the turn, so a glycine in the position avoids a clash. Position 2 would be a good fit for a proline, but is a different amino acid in this case.

In the <jmol>
<jmolLink>
<script>source /scripts/10/1072233/Alpha_2hmr/1.spt; background black; set zshade on; delay 0.5;
moveto 2.5 { -576 521 -629 104.96} 1076.13 -1.4 -15.1 {3.9860344827586216 57.429310344827584 10.870275862068969} 43.92085420330055 {0 0 0} 0 0 0 3.0 0.0 0.0;
source /scripts/10/1072233/Alpha_2hmr/6.spt; delay 1.0;select visible and alpha; backbone off; color cpk; draw * off
</script>
<text>second example</text>
</jmolLink>
</jmol>, we have a proline in position 3 and a cis-peptide between position 2 and 3. The cis-peptide has a shorter distance between alpha carbons (3.04 instead of 3.76 angstroms), making for a very tight turn. There is no hydrogen bond between residue 1 and 4 in this case. Beta turns involving a cis-peptide are classified as type VI.

You can revisit <scene name='10/1072233/Alpha_2hmr/4'>myohemerythrin</scene> and <scene name='10/1072233/Agglutinin/3'>agglutinin protein</scene>and <scene name='10/1072233/Tim/3'>TIM barrel protein</scene>. Use the button below to highlight glycine (white) and proline (green) residues.

<jmol>
<jmolButton>
<script>select gly.ca;
spacefill on;
color white;
select pro.ca;
spacefill on;
color green
</script>
<text>Glycine and Proline</text>
</jmolButton>
</jmol>

You can explore more turns at [https://betaturn.com/ betaturn.com], which allows you to browse for turns of a specific type, and contains a lot of information and explanations.

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</StructureSection>

Further reading
* [[Turns in Proteins]]
* [[Alpha helix]]
* [[Sheets in Proteins]]

==References==
<references/>

Lesson: beta turns

2025-05-09T15:05:38Z

Karsten Theis:

A '''beta turn''' is a secondary structure element consisting of four consecutive amino acids (or three consecutive peptide planes). The geometry of turns correspond to a change in the direction of the polypeptide backbone, with a short distance between the first and fourth alpha carbon.

==Concepts you can explore here==

# A beta turn is a secondary structure element distinct from (but sometimes overlapping with) alpha helices and beta strands
# Beta turns consist of stretches of four amino acids making a sharp turn, with a short distance between the first and last alpha carbon
# Beta turns typically occur near the surface of globular proteins, often connecting helices and strands
# There are multiple types of beta turns, distinguished by the torsion angles of the second and third residue
# Glycine and proline occur relatively often in beta turns and play distinct special roles

See the [[Talk:Lesson:_beta_turns|discussion tab]] for learning and teaching notes.

==Turns in 3D==

<StructureSection load='' size='[517,350]' side='right' caption='' scene='10/1072233/Turn_2mhr/2'>
===Basic features===
The interactive Jmol window on the right shows a beta turn (<scene name='10/1072233/Turn_2mhr/2'>reload initial scene</scene>) indicating the short distance between the first and the fourth alpha carbon. Because of this short distance, the polypeptide takes a sharp turn, sometimes also called a reverse turn. There are many types of beta turns, and they differ in the [[Tutorial:Ramachandran_principle_and_phi_psi_angles|phi and psi angles]] of residues two and three<ref>PMID:7756980</ref>. Some turns feature a <scene name='10/1072233/Turn_2mhr/4'>hydrogen bond</scene> between residues one and four (like the one shown here) and others don't.

===Beta turns in the context of other secondary structures===
The repetitive secondary structure elements ([[Alpha helix|alpha helices]] and [[Sheets in Proteins|beta strands]]) go in a single direction. Turns change the direction of the main chain, allowing them to connect alpha helices and beta strands at the surface of a globular protein. Of the six main chain hydrogen bonding partners of a turn, a maximum of two are engaged in hydrogen bonding, and turns are rarely found in the hydrophobic core. Below are three different protein folds highlighting the role of turns and their positions within a fold.

====Turns in an all-alpha protein====

In this <scene name='10/1072233/Alpha_2hmr/4'>myohemerythrin</scene> protein, you can see beta turns connecting the anti-parallel alpha helices. You can <jmol><jmolLink>
<script>
view1 = script("show moveto")[11][0];
select (67-70 and mainchain) or (68-69 and *.CB);
moveto 0.5 { 396 918 -22 24.97} 132.25 0.0 0.0 {27.01119230769231 33.81188461538462 10.03376923076923} 43.963541342342076 {0 0 0} 0 0 0 3.0 0.0 0.0;
wireframe 0.3;
color cpk;
select 67-70;
backbone off;
delay 0.5;
moveto 1.0 { 455 178 -872 110.43} 935.76 0.0 0.0 {26.793 33.036 8.6745} 44.96343106192573 {0 0 0} 0 0 0 3.0 0.0 0.0;
slab on
slab 60
delay 6;
select 67-70; backbone 0.4; wireframe off;
slab off;
script inline @{"moveto 1.0" + view1};
</script>
<text>zoom in</text>
</jmolLink>
</jmol> on the turn shown in the initial scene (and used below to explore conformations).

====Turns in an all-beta protein====
In this <scene name='10/1072233/Agglutinin/3'>agglutinin protein</scene>, you can see beta turns connecting the strands of anti-parallel beta sheets. Two antiparallel beta strands directly connected by a turn is called a <jmol><jmolLink>
<script>spin off; moveto 1.0 { 788 -362 -499 99.91} 404.55 0.0 0.0 {48.10615151515151 42.74112121212122 9.030939393939395} 37.460536158500446 {0 0 0} 0 0 0 3.0 0.0 0.0; delay 0.5; set zshade on; select protein; backbone -0.5;
</script>
<text>beta hairpin structure</text>
</jmolLink>
</jmol>. In this case, residues 1 and 4 of the turn are also part of the strands. This overlap of secondary structure assignment is common, but residues 2 and 3 of the turn are never part of a strand or an helix, by definition.

====Turns in an alpha/beta protein====

In this <scene name='10/1072233/Tim/3'>TIM barrel protein</scene>, you can see beta turns connecting helices and strands. The beta sheet is a barrel of parallel strands, as you can see if you turn on the cartoon representation with the buttons below.

The buttons below alow you to change the background color, spin the molecule, change the style and turn on the Ramachandran plot for 10 seconds.
<jmol>
<jmolButton>
<script>background white</script>
<text>white</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>background black</script>
<text>black</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>spin y -50</script>
<text>fastspin</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>spin off</script>
<text>spin off</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>select protein; cartoon on; backbone off</script>
<text>cartoon</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>select protein; backbone 0.5; cartoon off</script>
<text>trace</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>set zshade on; set zshadepower 2</script>
<text>zshade</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>save state ~one;
plot ramachandran; delay 10; restore state ~one</script>
<text>rama</text>
</jmolButton>
</jmol>

===Exploring torsion angles of turns===

The interactive Jmol window shows a <scene name='10/1072233/Turn_2mhr/1'>turn</scene> (residues 67-70 of the [[2hmr]] structure shown previously) that you can explore. Four consecutive amino acids are said to form a beta turn if the alpha carbon atoms of the first and the fourth residue are in close proximity (less than 7.0 or 7.5 Angstrom<ref>PMID:36293166</ref>). However, this also happens in alpha helices and 3(10) helices, and these are not classified as beta turn.

In the structure fragment shown, the alpha carbon atoms are numbered 1 through 4 (relative numbering, sometimes also given as n, n+1, n+2, n+3), and the distance between the carbonyl oxygen and the amide hydrogen is indicated (dashed line and magnitude). Side chains are truncated to just show the beta carbon, and residues 1 and 4 have some main chain omitted for clarity.

Another way of looking at it is that turns consist of three <jmol><jmolLink>
<script>
draw ID p68a polygon [{68.CA} {69.H} {69.CA}] color blue;
draw ID p68b polygon [{68.CA} {69.CA} {68.O}] color red;
draw ID p67a polygon [{67.CA} {68.H} {68.CA}] color blue;
draw ID p67b polygon [{67.CA} {68.CA} {67.O}] color red;
draw ID p69a polygon [{69.CA} {70.H} {70.CA}] color blue;
draw ID p69b polygon [{69.CA} {70.CA} {69.O}] color red;
delay 2; hide protein; delay 5; display protein; delay 1; draw ID p* delete;
</script>
<text>peptide planes</text>
</jmolLink>
</jmol>, whose relative orientation is determined by the phi/psi angles of residue 2 and 3.

The buttons below allow you to modify the conformation of the turn by changing the relevant torsion angles. To get a low energy conformation, you want a good hydrogen bond, i.e. carbonyl oxygen, amide hydrogen and nitrogen colinear <jmol>
<jmolLink>
<script>
define current selected;
select 67.O or 70.N or 70.H;
spacefill 30%;
selectionHalos on;
delay 1.5;
selectionHalos off;
spacefill off
select current;
</script>
<text>(☼)</text>
</jmolLink>
</jmol>, and want to avoid any clashes, e.g. carbonyl oxygen <jmol>
<jmolLink>
<script>
define current selected;
select *.O and visible;
spacefill 30%;
selectionHalos on;
delay 1.5;
selectionHalos off;
spacefill off
select current;
</script>
<text>(☼)</text>
</jmolLink>
</jmol> too close to beta carbon <jmol>
<jmolLink>
<script>
define current selected;
select *.CB and visible;
spacefill 30%;
selectionHalos on;
delay 1.5;
selectionHalos off;
spacefill off;
select current;
</script>
<text>(☼)</text>
</jmolLink>
</jmol> of the side chains.

====Excercise 1====

Turns have been classified into different types in different ways, but most classifications include type I, type II, and type I' <ref>PMID: 3184187</ref>. Try to use the buttons to make a type I turn with the features shown below. This is the most common beta turn (more than one third are of this type). Are there any clashes? How is the different from an alpha helix (where all carbonyl groups are pointing in the same direction)?

Before you start, make sure a single turn is displayed in the Jmol window on the right (<scene name='10/1072233/Turn_2mhr/1'>reload</scene>).

Phi&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {68.CA} {68.N} 10</script>
<text>+</text>
</jmolButton>
</jmol> 2 <jmol>
<jmolButton>
<script>rotate BRANCH {68.CA} {68.N} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {69.N}{69.CA} 10</script>
<text>+</text>
</jmolButton>
</jmol> 3 <jmol>
<jmolButton>
<script>rotate BRANCH {69.N}{69.CA} -10</script>
<text>−</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>save state ~one;
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
<text>Ramachandran</text>
</jmolButton>
</jmol>
Psi&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {68.C}{68.CA} 10</script>
<text>+</text>
</jmolButton>
</jmol> 2 <jmol>
<jmolButton>
<script>rotate BRANCH {68.C}{68.CA} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {69.CA}{69.C} 10</script>
<text>+</text>
</jmolButton>
</jmol> 3 <jmol>
<jmolButton>
<script>rotate BRANCH {69.CA}{69.C} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;&emsp;<jmol>
<jmolButton>
<script>original = {all}.xyz.all;rotate BRANCH {68.CA}{68.C} 180;rotate BRANCH {69.N}{69.CA} 180;rotate COMPARE {all} @original
</script>
<text>pepflip</text>
</jmolButton>
</jmol>

[[Image:Beta_turn_type_I.png|500px]]

====Excercise 2====

And now try to get a type I prime conformation, as shown below. This turn is rare (about 4% of beta turns are of this type). Hint: the pepflip button might serve as a bit of a shortcut. Why is that? Are there any clashes? If you had to choose, would you place a glycine at position 2 or position 3?

[[Image:Beta_turn_type_I_prime.png|500px]]

Before you start, make sure a single turn is displayed in the Jmol window on the right (<scene name='10/1072233/Turn_2mhr/3'>reload</scene>).

Phi&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {68.CA} {68.N} 10</script>
<text>+</text>
</jmolButton>
</jmol> 2 <jmol>
<jmolButton>
<script>rotate BRANCH {68.CA} {68.N} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {69.N}{69.CA} 10</script>
<text>+</text>
</jmolButton>
</jmol> 3 <jmol>
<jmolButton>
<script>rotate BRANCH {69.N}{69.CA} -10</script>
<text>−</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>save state ~one;
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
<text>Ramachandran</text>
</jmolButton>
</jmol>

Psi&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {68.C}{68.CA} 10;
</script>
<text>+</text>
</jmolButton>
</jmol> 2 <jmol>
<jmolButton>
<script>rotate BRANCH {68.C}{68.CA} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;<jmol>
<jmolButton>
<script>rotate BRANCH {69.CA}{69.C} 10</script>
<text>+</text>
</jmolButton>
</jmol> 3 <jmol>
<jmolButton>
<script>rotate BRANCH {69.CA}{69.C} -10</script>
<text>−</text>
</jmolButton>
</jmol>&emsp;&emsp;&emsp;<jmol>
<jmolButton>
<script>original = {all}.xyz.all;rotate BRANCH {68.CA}{68.C} 180;rotate BRANCH {69.N}{69.CA} 180;rotate COMPARE {all} @original
</script>
<text>pepflip</text>
</jmolButton>
</jmol>

====Exercise 3====
Compare and contrast the two turns we discussed, and compare them to alpha helix and beta sheet. Clicking the buttons will preserve the orientation of the 2->3 peptide plane <jmol>
<jmolLink>
<script>
define current selected;
select 68.C or 68.O or 69.N or 69.H;
spacefill 30%;
select 68.CA or 68.C or 68.O or 69.N or 69.H or 69.CA;
selectionHalos on;
delay 0.8;
selectionHalos off;
select 68.C or 68.O or 69.N or 69.H;
spacefill off;
select current;
</script>
<text>(☼)</text>
</jmolLink>
</jmol> while adjusting the torsion angles. You can press the last button to rotate the entire molecules as a rigid body (different from the pepflip button above, which changes torsion angles).

Before you start, make sure a single turn is displayed in the Jmol window on the right (<scene name='10/1072233/Turn_2mhr/3'>reload</scene>).

<jmol>
<jmolButton>
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;
rpsi2 = -30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA} @rpsi2;
rphi3 = -90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;
rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3;
set echo top center; echo "Type I"; color echo white</script>
<text>Type I</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -57 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -47 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -57 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -47 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "alpha helix"</script>
<text>(alpha helix)</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -49 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -26 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -49 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = -26 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "3-10 helix"</script>
<text>(3-10 helix)</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -140 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 130 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -140 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 130 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "beta strand"</script>
<text>(beta strand)</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = 60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 90 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type I prime"</script>
<text>Type I prime</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = 120 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = 80 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 0 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type II"</script>
<text>Type II</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>rphi2 = -60 - angle({67.C},{68.N},{68.CA},{68.C});rotate branch {68.CA} {68.N} @rphi2;rpsi2 = -30 - angle({68.N},{68.CA},{68.C},{69.N});rotate branch {68.C} {68.CA}@rpsi2;rphi3 = -120 - angle({68.C},{69.N},{69.CA},{69.C});rotate branch {69.N} {69.CA} @rphi3;rpsi3 = 120 - angle({69.N},{69.CA},{69.C},{70.N});rotate branch {69.CA} {69.C} @rpsi3; echo "Type VIII"</script>
<text>Type VIII</text>
</jmolButton>
</jmol>

<jmol>
<jmolButton>
<script>rotate X 180 180</script>
<text>rotate along x-axis</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>center visible</script>
<text>center</text>
</jmolButton>
</jmol> <jmol>
<jmolButton>
<script>save state ~one;
plot ramachandran; select 2.1 and 68; label 2; select 2.1 and 69; label 3; delay 5; restore state ~one</script>
<text>rama</text>
</jmolButton>
</jmol>

Here are some possible things to discuss: the orientation of the carbonyl groups, hydrogen bonding patterns, potential clashes of side chains with the main chain secondary structure conformation, regions of the Ramachandran plot, distance of certain pairs of atoms, cis and trans peptides (what?).

===Role of glycine and proline===

Glycine is the only amino acid lacking a side chain, allowing for a larger range of favorable phi/psi combinations. Proline, on the other hand, has a severely restricted range of phi torsion angles because it forms a five-membered ring involving the side chain and the main chain nitrogen. This allows these two amino acids to fulfil special roles in beta turns.

We will look at two examples from myohemethryin. The first shows a type II turn with <jmol>
<jmolLink>
<script>source /scripts/10/1072233/Alpha_2hmr/1.spt; background black; set zshade on; delay 0.5; moveto 1.0 { 68 -995 72 143.7} 132.25 0.0 0.0 {17.7825 49.4315 12.7155} 29.587605862640846 {0 0 0} 0 0 0 3.0 0.0 0.0;;
moveto 2.0 { 732 -555 394 175.75} 615.28 0.0 0.0 {15.7575 32.677 14.6085} 44.38762035414952 {0 0 0} 0 0 0 3.0 0.0 0.0;
source /scripts/10/1072233/Alpha_2hmr/2.spt; background black; set zshade on;delay 0.5;draw * off
</script>
<text>glycine in position 3</text>
</jmolLink>
</jmol>. A side chain in position 3 would clash with the carbonyl group of the central peptide plane of the turn, so a glycine in the position avoids a clash. Position 2 would be a good fit for a proline, but is a different amino acid in this case.

In the <jmol>
<jmolLink>
<script>source /scripts/10/1072233/Alpha_2hmr/1.spt; background black; set zshade on; delay 0.5;
moveto 2.5 { -576 521 -629 104.96} 1076.13 -1.4 -15.1 {3.9860344827586216 57.429310344827584 10.870275862068969} 43.92085420330055 {0 0 0} 0 0 0 3.0 0.0 0.0;
source /scripts/10/1072233/Alpha_2hmr/6.spt; delay 1.0;select visible and alpha; backbone off; color cpk; draw * off
</script>
<text>second example</text>
</jmolLink>
</jmol>, we have a proline in position 3 and a cis-peptide between position 2 and 3. The cis-peptide has a shorter distance between alpha carbons (3.04 instead of 3.76 angstroms), making for a very tight turn. There is no hydrogen bond between residue 1 and 4 in this case. Beta turns involving a cis-peptide are classified as type VI.

You can revisit <scene name='10/1072233/Alpha_2hmr/4'>myohemerythrin</scene> and <scene name='10/1072233/Agglutinin/3'>agglutinin protein</scene>and <scene name='10/1072233/Tim/3'>TIM barrel protein</scene>. Use the button below to highlight glycine (white) and proline (green) residues.

<jmol>
<jmolButton>
<script>select gly.ca;
spacefill on;
color white;
select pro.ca;
spacefill on;
color green
</script>
<text>Glycine and Proline</text>
</jmolButton>
</jmol>

You can explore more turns at [https://betaturn.com/ betaturn.com], which allows you to browse for turns of a specific type, and contains a lot of information and explanations.

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</StructureSection>

Further reading
* [[Turns in Proteins]]
* [[Alpha helix]]
* [[Sheets in Proteins]]

==References==
<references/>

User:Karsten Theis/AI tutorial

2025-05-08T18:05:53Z

Karsten Theis:

This is a tutorial for AI how to help with making 3D figures in Jmol (see all materials [https://github.com/ktheis/Jmol-Jane here]). If it helps humans too, so much the better.

<Structure load='' size='350' frame='true' align='right' caption='' scene='85/857774/Chymotrypsin/4' />

==My take on high-quality figures==

This is paraphrased from [[Image:Proteopedia_rubrics.pdf]].

A 3D figure should be content-rich, visually clear, fun to explore, and understandable. If it is part of a series of figures, they should work together well.

*Content-rich: If you can, tell a complete story in a single figure rather than having to click through multiple figures. Journal articles sometimes limit the number of figures to as low as 5, and so they are information-packed.

*Visually clear: There should be a clear sense of what the focus of the figure is (the foreground), and how this focal point connects to the whole (the background). There are multiple aspects that can help achieve a clear image (choice of initial zoom level, color, of representation, slabbing and fogging, line widths, initial orientation and center of rotation)

*Fun to explore: The viewer should be invited to rotate the figure and to zoom in and out. Interactive elements (hiding and displaying structural features, buttons to get back to the original view or to other standard views, animation, morphs) can guide this exploration, as well as [[Help:Viewing_pages|reminders]] about Proteopedia's and Jmol's built-in features (measure distances and angles, invitation to view in stereo, pop-out the image to maximize viewing area).

*Understandable: The viewer should be able to understand the visual elements (color coding, which representation for what) and the source of the data (PDB ID, typically) through the caption, legends on the viewing window, permanent and hover labels, and the text around the green link.

==Annotated scripts==
Here are some scripts. If you click on the title, you can see the resulting figure in the Jmol window above.

===Detailed views===
These have a focal point which should be centered and visible in the foreground. The focal point could be a ligand, an (empty) ligand binding site, an interface (e.g. dimer interface), a single interaction (e.g. disulfide bridge), or a single molecule. The background could be the entire remainder of the structure, or carefully selected parts of it, or blank (e.g. for a single molecule).

Typically, the foreground is shown at the detail of single atoms (represented by wireframe, spacefill, both "ball-and-stick", surfaces), and it is the center of rotation. Often, the background is shown with thinner lines, uniform color, or not showing single atoms but groups (represented by backbone, cartoon, meshribbon, ribbon, strand, trace, or surface). If the viewer is encouraged to rotate 360 degrees, the background should not interfere with seeing the foreground (use thin lines, slabbing, fading/fogging "zshade"). Transparency should be used with caution in Jmol because it can add visual clutter (spacefill and thick wireframe as well as cartoons add clutter, strands of constant thickness work well).

The <scene name='85/857774/Chymotrypsin/4'>initial scene</scene>: Chymotrypsin active site

<nowiki>
load =7GCH # Chymotrypsin with covalently bound inhibitor
restrict none # clean slate
define ~focal 57, 102, 195, LPF # foreground: catalytic triad and inhibitor
select LPF.C2 or 195.CB; bondOrder single; # ensure covalent bond
select ~focal; Spacefill 25%; wireframe 0.36 # ball-and-stick for foreground
center selected; zoom 300; #
select LPF.CP1, LPF.CP2, LPF.CP3, LPF.CP4, LPF.CP5, LPF.CP6; # aromatic ring of inhibitor
color atoms opaque [xda70d6]; # magenta
select LPF and not selected; color atoms opaque [xe6e6fa]; # rest of inhibitor: lavender???
select not ~focal; color chain; # default chain colors (pastel tones)
select protein and not ~focal; Spacefill 100%; # background as spacefill
select 57.CD2, 102.OD1, 195.CB; label "%n %r"; # labelled atoms
color label [x000000]; font label 13 SansSerif Bold; # white labels, chose font
select 57.CD2; set labelOffset -4 4; # each label has a different offset
select 102.OD1; set labelOffset 1 1; #
select 195.CB; set labelOffset 0 -1; #
background black; set zshade on # the background is almost not visible affects zshade
moveto 0.0 { -97 855 -510 89.56} 300.0 0.0 0.0 {38.343720000000005 74.45217999999998 85.45410000000003} 34.78371098010064 {0 0 0} 0 0 0 3.0 0.0 0.0;
</nowiki>

<scene name='10/1076814/Etransfer/1'>Electron transfer</scene>

<nowiki>
load "=1JRO" filter "biomolecule 2" # The structure contains 2 dimers, we are loading the second dimer
restrict none
define ~focal FES:E, FAD:E, MTE:F, MOS:F # Ligands involved in electron transfer (in chain E, F, not G, H)
select (sulfur and MTE:F) or MOS:E.MO; bondOrder single # show bond between sulfur atoms and molybdenum
select ~focal; wireframe 0.36; Spacefill 25% # ball-and-stick (atom colors default to CPK upon loading)
select 3001:E.S2 or 3002:E.FE1; label "Fe2S2"; color label [xffa500]; # label electron carriers
select FAD:E.O2; label "FAD" # label electron donor (color as atom)
select MOS:F.MO; label "MoCo" # label electron acceptor (color as atom)
select ~focal; set labelOffset 4 4; # offset for all labels
center visible; zoom 400; spin on # there is no good single view, so spin
set measurementUnits Angstroms # units for the measurements below
measure ([FAD]3005:E.C7M) ([FES]3002:E.S1) # shortest path for electrons
measure ([FES]3002:E.FE2) ([FES]3001:E.S2)
measure ([FES]3001:E.FE1) ([MTE]3003:F.C2)
</nowiki>

<scene name='80/804504/Dna/5'>Base stacking</scene>

<nowiki>
load =4c64
restrict none
define ~focal [DC]21:B or [DG]4:A # G:C base pair
select ~focal; wireframe 0.3; # show entire nucleotide (with backbone)
select sidechain and 5:A, 3:A, 20:B, 22:B; wireframe 0.2; color gray # stacking G:C and A:T base pair, just nucleobases
select 20:B or 5:A; color atoms opaque [xff7f50]; # coral # A:T base pair in coral

# The following shows the focal base pair as surface, with coloring indicating distance of closest stacked atom
set defaultVDW JMOL # sets Van der Waals radii
contact ID "contact1" ({(21:B or 4:A) and sidechain}) ({sidechain and (5:A, 3:A, 20:B ,22:B)}) surface;
contact ID "contact1" fill noMesh noDots notFrontOnly frontlit; # surface representation parameters
color $"contact1""roygb" range -0.5 1; # color scheme rainbow, with overlap in VdW radii in red

# Here is how to find the neighboring nucleobases (which are given explicitly in the "contact" command above)
# select within(3.8, ~focal and sidechain) and not (~focal or water)
# define ~neighbors within(group, selected) and sidechain

center visible; zoom 250

</nowiki>

<scene name='10/1076814/Intercalation/1'>Intercalation</scene>

<nowiki>
load =3k5y # RNA bound to protein
restrict none
select protein and sidechain and within(3.5, RNA and sidechain); # protein side chain atoms that are close to nucleobases
select within(group, selected) and (alpha or sidechain); wireframe 0.3; # entire side chain plus alpha carbon shown
select selected and (alpha or *.CB); color bond gray; # fix bond color between alpha and beta carbon to uniform gray
select alpha; backbone on; color chain # entire protein shown as thin backbone
select RNA and sidechain; Spacefill 100%; color atoms red; # Nucleobases shown as red spacefilling (this is the focus of the figure)
select RNA and mainchain; Spacefill 0.5; # rest of RNA shown as ball...
select RNA; wireframe 0.3; # and stick (it's fine to show nucleobases as wireframe, too, gets occluded)
center RNA; zoom 200 # center of rotation is RNA so it stays in view
</nowiki>

<scene name='10/1076814/Nagal_galsa_superposition/1'>Superposition</scene>

<jmol>
<jmolCheckbox>
<scriptWhenUnChecked>animation off; model 0
</scriptWhenUnChecked>
<scriptWhenchecked>animation mode loop; animation on
</scriptWhenchecked>
<checked>false</checked>
<text>animation</text>
</jmolCheckbox>
</jmol>

<nowiki>
load files "=3H54" "=3LX9" # load 2 files, they are selected as 1.1 and 2.1 below
restrict none # display is cleared
define ~act2 2.1 and (47,92,93,134,142,168,170,172,203,206,207,227,231) and *:A # active site residues of 3LX9
define ~act1 1.1 and (33,78,79,119,127,154,156,158,188,191,192,213,217) and *:A # active site residues of 3H54
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{~act2}{~act1} ROTATE TRANSLATE # superposition (different sequences, so use alpha carbon)
set ssbonds SIDECHAIN # disulfide bonds are anchored on SG, not on CA

set traceAlpha TRUE
set zshade on
set sheetSmoothing 0.3

# drawing 3H54 active site
select 1.1 and ~act1 and (sidechain or *.CA); wireframe 60; # show the active site as wireframe
color bonds cornflowerblue # 3H54 is shown in blue (just the bonds)
select selected and not _C; spacefill 80; color cpk # spacefill, atoms other than carbon shown using CPK color scheme
select 1.1 and (32-34, 77-80, 118-120, 126-128, 153-159, 187-193, 212-218) and *:A.CA;# some main chain context for the active site residues
trace 10; color cornflowerblue # show as trace in blue
select 1.1 and 1000:A; wireframe 60; # selecting the sugar in 3H54
select selected and _C; color skyblue; # carbons in skyblue

# drawing 3LX9 active site
select 2.1 and ~act2 and (sidechain or *.CA); wireframe 60; # show the active site as wireframe
color bonds yellow # 3LX9 is shown in yellow (just the bonds)
select selected and not _C; spacefill 80; color cpk # spacefill, atoms other than carbon shown using CPK color scheme
select 2.1 and (46-48, 91-94, 133-135, 141-143, 167-173, 202-208, 226-232) and *:A.CA;# some main chain context for the active site residues
trace 10; color yellow # show as trace in yellow
select 2.1 and 1000:A; wireframe 60;; # selecting the sugar in 3LX9
select selected and _C; color beige; # carbons in beige
center selected; zoom 300 # center and zoom in
</nowiki>

And here are the commands for turning animation on or off (used in the checkbox above):

<nowiki>
animation off; model 0 # show both models
animation mode loop; animation on # animate between the models
</nowiki>

<scene name='10/1076814/Trypsin_ryan_nini/2'>Trypsin</scene>
<nowiki>
load =2PTC
restrict none
# active site and pocket of enzyme as well as
# lysine and cystine of inhibitor are featured here
define ~focal 14:I, 15:I, 38:I, 57:E, 102:E, 195:E, 189:E
select ~focal and (sidechain or alpha); wireframe 0.2; spacefill 0.4; # ball-and-stick for focus
select protein and not (1-15 and chain=I); backbone 0.5 # leave out 15-16 in chain=I
select protein and (1-15 and chain=I); backbone 0.5 # this is a hack to ...
connect (15:I.CA)(16:I.CA) radius 0.52 create # get one backbone segment
select 15:I.CA or 16:I.CA; color bond white # in a different color
select nitrogen; color atoms opaque [x002da6]; # CPK-like palette for side chains
select oxygen; color atoms opaque [xa6243a];
select sulfur; color atoms opaque [xffff00];

# slightly more intense color than backbone for carbons in side chains
select alpha and chain=E; color atoms opaque [x5a91b8];
select alpha and chain=I; color atoms opaque [xfb8a8a];
select ~focal and chain=E and carbon and sidechain; color atoms opaque [x96e1fb]
select ~focal and chain=E and (*.CA or *.CB); color bond [x96e1fb]
select ~focal and chain=I and carbon and sidechain; color atoms opaque [xfa6563];
select ~focal and chain=I and (*.CA or *.CB); color bond [xfa6563]

#hydrogen bonds in catalytic triad
select (57:E or 195:E or 102:E) and sidechain
set hbondsRasmol FALSE; calculate HBONDS; hbonds 0.1

#the dark purple background in combination with zShade gives good depth feeling for this color palette
background [x3d2b49];
set zShadePower 2; set zShade true;

#slab removes a loop that interferes with view into active site in the initial orientation
moveto 0.0 { 124 277 953 167.49} 300.0 0.0 0.0 {11.051 74.132 19.27} 38.73 {0 0 0} 0 0 0 3.0 0.0 0.0;
slab 60;depth 0;slab on;
</nowiki>

<scene name='10/100139/Spacefill/1'>Green fluorescent protein</scene>

<nowiki>
load =1ema
# define the central helix in GFP and the hydrophobic residues lining it
define ~helix 57-71
define ~hydrophobic_liner 12, 14, 16, 18, 22, 27, 29, 42, 44, 46, 48, 98, 100, 110, 112, 114, 119, 123, 125, 150, 152, 161, 163, 165, 167, 179, 201, 207, 220, 224, 226

# Show a translucent ribbon for context (some of the colors are overridden later)
select all
Ribbon on;
color atoms translucent 128 [xf0f8ff]; # aliceblue

# The helix is shown as solid red spacefill
select ~helix
Spacefill 100%
color atoms opaque [xdc143c]; # crimson

# The side chains lining it are shown as solid whitish spacefill
select sidechain and ~hydrophobic_liner
color atoms opaque [xf0f8ff]; # aliceblue
Spacefill 100%
</nowiki>

===Overall views===
These don't have a focal point. They should be centered on everything displayed. If using a representation you can look through (e.g. backbone or cartoon rather than surface or spacefill), fading/fogging "zshade" may be helpful to distinguish front and back.

<scene name='78/780454/Domains/7'>Domains</scene>

<nowiki>
load =1d9z # UvrB, a helicase-like protein bound to ATP
restrict none
select protein; color gold; cartoon on # The gold domain has most segments, so make everything gold
select not helix and not sheet; cartoon 0.3 # Make coils a bit thicker than default for balance and visibility
select 415-595; color red
select 157-244; color blue
select 91-116; color aqua # beta hairpin, unique to UvrB
select 245-324, 349-378; color lime # UvrA interaction domain
select MG, ATP, ZN; color silver; spacefill 100% # Ligands in spacefill (Zn is crystallization artifact)
</nowiki>

<scene name='10/1071246/Trypsin_5mop/5'>Rainbow plus surface</scene>

<nowiki>
load =5mop # trypsin
restrict none
select protein; cartoon on; color group # rainbow cartoon
select protein and (57,195) and sidechain and not hydrogen; color cpk; spacefill 25% # ball ...
select protein and (57,195) and (sidechain or alpha) and not hydrogen; wireframe 0.36 # ...and stick
select protein; isosurface ID "1" SASURFACE # solvent-accessible surface
color isosurface translucent 0.875 white # white and translucent
isosurface ID "1" fill noMesh noDots notFrontOnly frontlit # these settings help to see the cartoon
select all; set hoverLabel "%n %R"; # residue numbers and name
select [CA]; set hoverLabel "Calcium"; # spell out "calcium" to distinguish from alpha-carbon
</nowiki>

User:Karsten Theis/Molecular Playground

2025-05-06T14:25:23Z

Karsten Theis:

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

<html5media height="337" width="600">https://www.youtube.com/watch?v=gzlKHNoZdYc</html5media>

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

What should you check before you save an existing scene?

# Make sure the parts of interest stay in view as you rotate the molecule
# Decide whether your background should be black (works well) or something else
# Choose a descriptive file name

What are the advantages of creating and loading a pngj file?

# It contains everything Jmol needs for the initial scene, including the coordinates
# It preserves the orientation
# It has a built-in preview that works without Jmol

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console). Complex visualizations might be slower here than on molecular playground because the Jmol application is more powerful than the applet used in the browser.

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[1024,693]' frame='true' align='right' caption='' scene='' />

<jmol>
<jmolLink>
<script> script /images/5/5e/Benzene_cyclohexane.spt
</script>
<text>Cyclohexane vs Benzene</text>
</jmolLink>
</jmol>

<jmol>
<jmolLink>
<script> script /images/c/c6/Cellulose.spt
</script>
<text>Cellulose</text>
</jmolLink>
</jmol>

File:Cellulose.spt

2025-05-06T14:24:04Z

Karsten Theis: Molecular Playground script, cellulose

== Summary ==
Molecular Playground script, cellulose
== Licensing ==
{{self|cc-by-3.0}}

File:Cellulose.pngj

2025-05-06T14:07:33Z

Karsten Theis: Opening scene for cellulose molecular playground exhibit.

== Summary ==
Opening scene for cellulose molecular playground exhibit.
== Licensing ==
{{self|cc-by-3.0}}

User:Karsten Theis/Molecular Playground

2025-05-06T14:06:18Z

Karsten Theis: /* Sandbox */

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

<html5media height="337" width="600">https://www.youtube.com/watch?v=gzlKHNoZdYc</html5media>

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

What should you check before you save an existing scene?

# Make sure the parts of interest stay in view as you rotate the molecule
# Decide whether your background should be black (works well) or something else
# Choose a descriptive file name

What are the advantages of creating and loading a pngj file?

# It contains everything Jmol needs for the initial scene, including the coordinates
# It preserves the orientation
# It has a built-in preview that works without Jmol

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console). Complex visualizations might be slower here than on molecular playground because the Jmol application is more powerful than the applet used in the browser.

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[1024,693]' frame='true' align='right' caption='' scene='' />

<jmol>
<jmolLink>
<script> script /images/5/5e/Benzene_cyclohexane.spt
</script>
<text>Cyclohexane vs Benzene</text>
</jmolLink>
</jmol>

User:Karsten Theis/Molecular Playground

2025-05-06T13:02:39Z

Karsten Theis:

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

<html5media height="337" width="600">https://www.youtube.com/watch?v=gzlKHNoZdYc</html5media>

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

What should you check before you save an existing scene?

# Make sure the parts of interest stay in view as you rotate the molecule
# Decide whether your background should be black (works well) or something else
# Choose a descriptive file name

What are the advantages of creating and loading a pngj file?

# It contains everything Jmol needs for the initial scene, including the coordinates
# It preserves the orientation
# It has a built-in preview that works without Jmol

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[1024,693]' frame='true' align='right' caption='' scene='' />

<jmol>
<jmolLink>
<script> script /images/5/5e/Benzene_cyclohexane.spt
</script>
<text>Cyclohexane vs Benzene</text>
</jmolLink>
</jmol>

User:Karsten Theis/Molecular Playground

2025-05-06T12:49:30Z

Karsten Theis: /* First scene */

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

<html5media height="337" width="600">https://www.youtube.com/watch?v=gzlKHNoZdYc</html5media>

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

What should you check before you save an existing scene?

# Make sure the parts of interest stay in view as you rotate the molecule
# Decide whether your background should be black (works well) or something else
# Choose a descriptive file name

What are the advantages of creating and loading a pngj file?

# It contains everything Jmol needs for the initial scene, including the coordinates
# It preserves the orientation
# It has a built-in preview that works without Jmol

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[1024,693]' frame='true' align='right' caption='' scene='' />

User:Karsten Theis/Molecular Playground

2025-05-06T12:47:26Z

Karsten Theis:

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

<html5media height="337" width="600">https://youtu.be/gzlKHNoZdYc</html5media>

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

What should you check before you save an existing scene?

# Make sure the parts of interest stay in view as you rotate the molecule
# Decide whether your background should be black (works well) or something else
# Choose a descriptive file name

What are the advantages of creating and loading a pngj file?

# It contains everything Jmol needs for the initial scene, including the coordinates
# It preserves the orientation
# It has a built-in preview that works without Jmol

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[1024,693]' frame='true' align='right' caption='' scene='' />

User:Karsten Theis/Molecular Playground

2025-05-06T12:44:30Z

Karsten Theis: /* First scene */

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

https://youtu.be/gzlKHNoZdYc

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

What should you check before you save an existing scene?

# Make sure the parts of interest stay in view as you rotate the molecule
# Decide whether your background should be black (works well) or something else
# Choose a descriptive file name

What are the advantages of creating and loading a pngj file?

# It contains everything Jmol needs for the initial scene, including the coordinates
# It preserves the orientation
# It has a built-in preview that works without Jmol

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[1024,693]' frame='true' align='right' caption='' scene='' />

User:Karsten Theis/Molecular Playground

2025-05-06T12:34:37Z

Karsten Theis:

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

What should you check before you save an existing scene?

# Make sure the parts of interest stay in view as you rotate the molecule
# Decide whether your background should be black (works well) or something else
# Choose a descriptive file name

What are the advantages of creating and loading a pngj file?

# It contains everything Jmol needs for the initial scene, including the coordinates
# It preserves the orientation
# It has a built-in preview that works without Jmol

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[1024,693]' frame='true' align='right' caption='' scene='' />

User:Karsten Theis/Molecular Playground

2025-05-05T15:36:43Z

Karsten Theis: /* First scene */

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

What should you check before you save an existing scene?

# Make sure the parts of interest stay in view as you rotate the molecule
# Decide whether your background should be black (works well) or something else
# Choose a descriptive file name

What are the advantages of creating and loading a pngj file?

# It contains everything Jmol needs for the initial scene, including the coordinates
# It preserves the orientation
# It has a built-in preview that works without Jmol

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />

User:Karsten Theis/Molecular Playground

2025-05-05T15:31:10Z

Karsten Theis:

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA", http://jmol.x3dna.org/ for nucleic acids and complexes.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />

User:Karsten Theis/Molecular Playground

2025-05-03T17:42:31Z

Karsten Theis:

This is a sketch how to create content for the [[Molecular Playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA",

User:Karsten Theis/Molecular Playground

2025-05-03T17:42:01Z

Karsten Theis:

This is a sketch how to create content for the [[molecular playground]].

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA",

User:Karsten Theis/Molecular Playground

2025-05-03T17:40:43Z

Karsten Theis:

== Project name ==
Choose a project name, for example UvrB_1d9z. In the example, I combined the protein name with the PDB ID code of the coordinates I am showing.

== First scene ==
The easiest way to get started is with an existing Jmol scene (from Proteopedia, First Glance or from other sources - just make sure you have the rights to it). In the Jmol window, right-click somewhere on the top, and choose "console" from the menu. Then, type "write project_name.pngj" and save the file. This contains the coordinates and the drawing commands.

Then, start on your script file, named "project_name.spt". It could be as simple as:

<nowiki>
load UvrB_1d9z.pngj
spin on
</nowiki>

This assumes that your "UvrB_1d9z.pngj" file is in the same folder as the script file, "UvrB_1d9z.spt", which is how the molecular playground is set up.

== Banner ==
There is space for limited text at the top of the display, called the banner. We will add one command to set the banner to "DNA repair protein UvrB":

<nowiki>
load UvrB_1d9z.pngj
message driver:DNA repair protein UvrB
spin on
</nowiki>

When running in the molecular playground, the banner is also used to give feedback when the viewers hands are detected for rotation and zoom. This minimal file is ready for the molecular playground, but we will expand it a bit for testing.

== Testing online or offline ==
With a little bit of extra work, we can write a script that you can test online and share (by posting on Proteopedia, for example), or run locally. You will see the line "if (_applet)" below, which checks if Jmol is running in an applet (i.e. is online). Here is the updated script:

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

banner("DNA repair protein UvrB")
spin on
</nowiki>

For the applet, the URLs are given in their complete form, so they should work on Proteopedia and on other platforms. Try opening up [https://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jmol Simple], clicking on console, and pasting the code above to test.

To test this in a molecular playground installation, you have to copy the *.pngj and the *.spt files into the assets folder, and ask the admin to add the project to one of the play lists.

To run it on Proteopedia, you upload the script, edit a page to make a rectangular window and add a Jmol link with the script in it (go to the sandbox below to test it without the need to log in):

<nowiki>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />
<jmol>
<jmolLink>
<script> script /images/6/65/UvrB_1d9z.spt</script>
<text>UvrB, a helicase adapted for DNA repair</text>
</jmolLink>
</jmol>
</nowiki>

You can find working examples [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here].

== Summary ==

Here are the steps without using Proteopedia:
# Create an initial scene as PNGJ file
# Create a script loading the initial scene (plus other commands, if desired)
# Give both files to the Molecular Playground administrator

Here are the steps with Proteopedia:
# Create an initial scene as PNGJ file, upload to Proteopedia and note the URL
# Create a script loading the initial scene using the URL, upload to Proteopedia and note the URL
# Call the script in a jmolLink on a page with a rectangular Jmol window

== Creating a tour ==

We can expand the single-scene-script to show off the molecule. Below is the finished script, which you can try [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. The first part is the same as the UvrB_1d9z script, up until the "# Guided tour ..." comment. The rest of the script goes to different views, changes the banner text and lets the viewer explore.

<nowiki>
if (_applet) {
script https://proteopedia.org/wiki/images/6/65/Molecular_playground_helpers.spt
load https://proteopedia.org/wiki/images/f/f6/Uvrb_1d9z.pngj
} else {
script Molecular_playground_helpers.spt
load UvrB_1d9z.pngj
}

# Guided tour, showing 3 features of UvrB
antialiasDisplay=false; cartoonFancy=false; antialiasDisplayFlag=false #faster rotation

banner("UvrB, a DNA repair helicase [PDB ID 1d9z]")
spin on # Start with spinning molecule so the 3D nature is clear
delay 5
spin off
moveto 1.0 { -844 -132 520 125.23} 300.0 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("bound ATP")
delay 2
select ATP; color cpk
delay2play(5) # delays 5 seconds plus the time viewer rotates/zooms the structure
banner("DNA binding clamp in cyan")
moveto 1.0 { -905 -349 244 137.3} 260.87 0.0 0.0 {64.70854666666669 12.864631111111102 63.586506666666644} 64.2453671308168 {0 0 0} 0 0 0 3.0 0.0 0.0;
delay 2
delay2play(5)
moveto 1.0 { -732 -239 637 116.38} 260.87 0.0 0.0 {58.64131184407797 19.068823088455765 30.446964017990993} 81.87433897489076 {0 0 0} 0 0 0 3.0 0.0 0.0;
banner("UvrA binding domain ([1t5l] has corrected fold)")
delay 2
delay2play(5)
moveto 1.0 { -850 23 526 128.87} 115.0 0.0 0.29 {56.569378268323966 31.076560437205238 59.530780111444614} 51.673541253257795 {0 0 0} 0 0 0 3.0 0.0 0.0;
antialiasDisplay=true; cartoonFancy=true; antialiasDisplayFlag=true #nicer rendering
banner("Thanks for watching")
</nowiki>

The "moveto 1.0" commands change the orientation. You can manually change the orientation (and centering and zoom) to something you like, and then write "show moveto" in the Jmol console. This gives you the command to copy and paste into your script. You can also use the console to select the feature of interest ("select ATP"), and then issue the command "center selected" to center automatically. Again, you would issue "show moveto" to get the orientation, and paste it into your script.

The "banner()" function changes the banner and the "delay" function waits until proceeding to the next step. The "delay2play()" function is a bit more complex. It monitors the orientation of the molecule. As long as the viewer changes the orientation, it will not proceed in the script. Once the viewer is done interacting for a prescribed number of seconds, it goes back to the orientation it had before the viewer interaction, and proceeds with the script.

There is only one command that changes the scene, "select ATP; color CPK". It changes the color of the bound ATP from silver to CPK (a color scheme giving unique colors to each chemical element). You can have lots of other commands in your script, even loading a new set of coordinates (or new PNGJ file). You can get as fancy as Jmol allows, which is pretty fancy.

An example for a more complex script is also [https://proteopedia.org/wiki/index.php/User:Karsten_Theis/Sandbox_2 here]. It uses a picture as background, and switches between the two molecules, cyclohexane and benzene.

== Sandbox ==

You can use this space to load a PNGJ file (right-click, "file > load > open local file") and start finding good viewing orientations or testing Jmol commands (via console).

<jmol>
<jmolButton>
<script>console</script>
<text>Open console</text>
</jmolButton>
</jmol>
<Structure load='' size='[800,600]' frame='true' align='right' caption='' scene='' />

== FAQ ==
* Why use the PNGJ file? It has the advantage of saving everything in a single file (coordinates, state, additional information case-by-case such as electron density, surfaces, background image, etc.). It also makes it easy to adopt scenes that are already made. Alternatively, you could just load a PDB file, and script everything else, which is nice for others learning how to script Jmol.
* Why do we need a rectangular canvas? Traditionally, the Jmol canvas is square (makes sense for rotating molecules, round would be even better). However, the Molecular Playground uses a projector with 4:3 aspect ratio, and it makes sense to build content starting with that aspect ratio. Granted, the banner uses some of that, so the real aspect ratio is a bit different.
* What are good sources for the initial scene? First Glance in Jmol (check out the electron density), Proteopedia, Molecule of the Month (RCSB or for small molecules [https://www.chm.bris.ac.uk/motm/motm.htm Bristol], Google e.g. "jmol DNA",