Jmol/Superposition: Difference between revisions

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]].

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:

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.

The jmol command to superimpose structures is called "compare", and it has a lot of parameters. Here is an example:

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.