measure phi/psi/chi/omega angles

[tic20@…]

Add Chimera1-like support for getting/setting phi/psi/chi/omega angles. Use C++ layer for performance.

First step would be implementing changing torsion angles.

[pett]

from Tristan:

A few other thoughts on this. You’ll probably find my Rotamer class useful. For most residues you can’t expect MD to find the “correct” conformation starting from a random rotamer - you’re going to need to select the most likely one (based on criteria like clashes, H-bonding etc.). My Rotamer_Mgr maintains a dictionary of rotamers found in the real world, including a standard deviation for each chi dihedral (from the MolProbity dataset). I also have the code (albeit not yet ported over from my old Rotamer implementation) to cycle the atomic coordinates through each ideal rotamer (by sequentially rotating about each dihedral - so the starting coordinates do need to be reasonable). Could do with some generalisation (I took the easier approach of just spelling out the names of the atoms that move when each torsion rotates), but it’s there.

[pett]

Residue phi/phi/omega/chi1-4 angles can be get/set via corresponding Residue attributes. Not optimized, but it seems that Tristan has already implemented highly optimized code of his own that accomplishes what he needs efficiently.

[tic20@…]

Well, I have highly optimized code for *reading* dihedral angles, and some somewhat-more-clunky code for setting sidechain chi angles (and nothing for setting phi/psi/omega). Will have to check it out!

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY