Jmol/Superposition: Difference between revisions
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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: | 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> | <nowiki> | ||
load files "=3HG5" "=3H54"</nowiki> | load files "=3HG5" "=3H54" | ||
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). | 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== | ==Equivalent atoms== | ||
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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 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== | ==Compare command== | ||
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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. | 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== | ==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. | 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> | <nowiki> | ||
model 0 | |||
select protein and 1.1; cartoon; color palegreen; center selected | select protein and 1.1; cartoon; color palegreen; center selected | ||
select protein and 2.1; cartoon; color cornflowerblue;</nowiki> | select protein and 2.1; cartoon; color cornflowerblue;</nowiki> | ||
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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. | 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== | ==Demonstration== | ||
<StructureSection load='3hg5' size='340' side='right' caption='' scene=''> | <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/ | 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> | <jmol> | ||
<jmolButton> | <jmolButton> | ||
