User:Karsten Theis/AI tutorial: Difference between revisions

(22 intermediate revisions by the same user not shown)

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This is a tutorial for AI how to help with making 3D figures in Jmol. If it helps humans too, so much the better.

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.

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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 initial scene: Chymotrypsin active site

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

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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 (~~aquarell~~)

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

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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>

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>

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>

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>

<scriptWhenUnChecked>animation off; model 0

</scriptWhenUnChecked>

<scriptWhenchecked>animation mode loop; animation on

</scriptWhenchecked>

<checked>false</checked>

<text>animation</text>

</jmolCheckbox>

</jmol>

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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

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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, ~~169~~-173, 202-208, 226-232) and *:A.CA;# some main chain context for the active site residues

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

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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):

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>

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>

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>

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>

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/AI tutorial: Difference between revisions

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@@ Line 1: / Line 1: @@
-This is a tutorial for AI how to help with making 3D figures in Jmol. If it helps humans too, so much the better.
+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' />
@@ Line 25: / Line 25: @@
 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 initial scene: Chymotrypsin active site
+The <scene name='85/857774/Chymotrypsin/4'>initial scene</scene>: Chymotrypsin active site
   <nowiki>
@@ Line 37: / Line 38: @@
 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 (aquarell)
+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
@@ Line 47: / Line 48: @@
 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>
@@ Line 56: / Line 132: @@
 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
@@ Line 70: / Line 150: @@
 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, 169-173, 202-208, 226-232) and *:A.CA;# some main chain context for the active site residues
+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
@@ Line 76: / Line 156: @@
 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>