When I make a mutagenesis using pymol, I am faced with several questions:
1. When I do it, which should I choose, Backbone-Dependent or Backbone-Independent?
2. What does the percentage indicate in red line sign of the picture and how to select the rotamer for my sturcture based on the percent （96%，11%，2.2%） or not?
- The mutagenesis tools use a rotamer library for proposing different structures. Backbone dependent rotamer libraries assign probabilities for each rotamer as a function of the phi and psi backbone dihedral angles (typically by using bins of 10 degrees on phi and psi angles). Backbone independent rotamer libraries disregard the phi and psi dependencies and are typically used to model amino acids that are not part of a polypeptide chain, as well as N or C terminal amino acids. The default rotamer library is provided by the chempy/sidechains/sc_bb_dep.pkl file, but you can use another library if necessary.
- Red percentages show the proportion of structures with that particular rotamer out of the population sampled (either the backbone bin or for the residue type as a whole).
http://www.swisssidechain.ch/FAQ.php#What_are_rotamers
http://sourceforge.net/p/pymol/mailman/message/11670932/
Hi Jerome, you said that it is possible to use another library if necessary. I saw that chempy imports the rotamer library from "bbind02.May.lib" file. However, it does so by using the urllib.py script to access that file (i.e., the file isn't available in my computer). In short, I have not managed to find a way to update the rotamer library used by default in pymol. Do you know how this can be achieved?
Hi Diogo,
You can take a look at the following file:
modules/pymol/wizard/mutagenesis.py
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