Jmol/Superposition: Difference between revisions
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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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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]] 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 [[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== | ||