Backbone-Dependent Rotamer library (Dunbrack, Cohen see ref) is imported into pymol giving access to this information. There are a number of different ways to use the data, I've only implemented a few as well as added extra functions that seemed useful.
- colorRotamers - color rotamers by closest matching rotamer angles from database; i.e. color by how common each rotamer of selection, blue - red (least to most common).
- Rotamer Menu - an added menu into menu.py, which displays the most common rotamers for the given(clicked) residue; you can also set the residue any of the common rotamers as well
- set_rotamer - routine called by above menu, but can be called manually to set a specific residues side-chain angles
- set_phipsi - set all phi,psi angles of given selection to given angles (useful for creating secondary structures)
To setup a rotamer menu inside the residue menu:
- copy rotamers.py to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/rotamers.py
- copy mymenu.py to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/menu.py (WARNING : overwrites default menu.py - use at your own risk)
- copy bbdep02.May.sortlib to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/bbdep02.May.sortlib (or newer version of sorted bbdep)
This is only one possible way to do this, I am sure there are many others.
colorRotamers selection set_rotamer selection, chi1_angle [,chi2_angle] [,chi3_angle] [,chi4_angle] set_phipsi selection phi_angle, psi_angle
Scripts (Rotamers.py ; MyMenu.py)
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Dunbrack and Cohen. Protein Science 1997