Rotamer Toggle

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DESCRIPTION

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.

USAGE

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)

EXAMPLES

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SEE ALSO

REFERENCES

Dunbrack and Cohen. Protein Science 1997

Dunbrack Lab Page (Contains backbone-dependent library)