The wt_vs_mut plugin makes it easy to visualize the difference between two similar protein structures. The plugin automatically finds all the residues that differ between the two structures, then it lets the user zoom in on the interactions being made by those residues one at a time. The purpose of this is to let the user judge the effect that each mutation might have on one structure or the other. This plugin was originally written to help with the manual validation step of a protein design project, but is quite general and should be useful in many other contexts as well.
Start by downloading the wt_vs_mut.py file somewhere on your computer. The
entire plugin is contained in this file to make installation easier. Then, in
pymol, open the two structures you want to compare. I'll assume one is called
wildtype and the other is called mutant. Enter the following two commands:
run /path/to/wt_vs_mut.py
wt_vs_mut wildtype, mutant
Of course, path/to/wt_vs_mut.py is the path to wherever you downloaded the
plugin, relative to wherever pymol is running. The first command installs the
plugin. You'll have to type it every time you run pymol unless you put it in
your ~/.pymolrc file. The second command starts the plugin. Once the plugin
is started, it will zoom in on the first difference between the two structures
and show all the sidechains within a few angstroms. Press [Ctrl-Space] and it
will zoom to the next difference and show the same thing.
Note that this plugin requires at least version 1.7 of pymol. Older versions don't have a recent enough distribution of python. If you run into other troubles or would like to suggest a new feature, feel free to submit an issue through the GitHub GUI.