PS. Please note, that for some of the features mentioned you will need the latest cctbx version, preferably fresh check-out from svn. Oleg. On Mon, Sep 21, 2015 at 9:49 AM, Oleg Sobolev wrote:

Hi Nicholas,

First, the most basic way to calculate torsion (dihedral) angle for 4 given atoms is: from scitbx.math import dihedral_angle angle = dihedral_angle(sites=[(1,0,0), (0,0,0), (0,1,0), (1,1,0)], deg=True) where 'sites' contain atom coordinates.

Second, here is more high-level way to get phi-psi angles: from mmtbx.conformation_dependent_library import generate_protein_threes pdb_h = iotbx.pdb.hierarchy.input(file_name=args[0]).hierarchy sites_cart = pdb_h.atoms().extract_xyz() # Note that this is a generator for three in generate_protein_threes( hierarchy=pdb_h, geometry=None): proxies = three.get_dummy_dihedral_proxies() for p in proxies: print "angle=", dihedral_angle( sites=[sites_cart[x] for x in p.i_seqs], deg=True)

Third, to get all proxies, use this function with hierarchy: from mmtbx.geometry_restraints.torsion_restraints.utils import \ get_complete_dihedral_proxies dih_proxies = get_complete_dihedral_proxies( pdb_hierarchy=pdb_h)

Hope this helps, full script is below and attached (run with pdb file as the only argument).

Best regards, Oleg Sobolev.

import sys from scitbx.math import dihedral_angle import iotbx.pdb import os.path

def basics(): print "Basics:" angle = dihedral_angle(sites=[(1,0,0), (0,0,0), (0,1,0), (1,1,0)], deg=True) print "Angle:", angle angle = dihedral_angle(sites=[(2,1,1), (0,0,0), (0,1,0), (1,1,0)], deg=True) print "Angle in degrees:", angle angle = dihedral_angle(sites=[(2,1,1), (0,0,0), (0,1,0), (1,1,0)], deg=False) print "Angle in radians:", angle print "="*50

def advanced(args): print "Advanced phi-psi:" if len(args) != 1 or not os.path.isfile(args[0]): print "Bad argument" return

# phi-psi angles from mmtbx.conformation_dependent_library import generate_protein_threes pdb_h = iotbx.pdb.hierarchy.input(file_name=args[0]).hierarchy sites_cart = pdb_h.atoms().extract_xyz() n_proxies = 0 # Note that this is a generator for three in generate_protein_threes( hierarchy=pdb_h, geometry=None): proxies = three.get_dummy_dihedral_proxies() for p in proxies: for i_seq in p.i_seqs: print pdb_h.atoms()[i_seq].id_str(), print "angle=", dihedral_angle( sites=[sites_cart[x] for x in p.i_seqs], deg=True) n_proxies += 1 print "Total angles:", n_proxies

def all_dihedral_proxies(args): print "Advanced all:" if len(args) != 1 or not os.path.isfile(args[0]): print "Bad argument" return # all angles: from mmtbx.geometry_restraints.torsion_restraints.utils import \ get_complete_dihedral_proxies

pdb_h = iotbx.pdb.hierarchy.input(file_name=args[0]).hierarchy sites_cart = pdb_h.atoms().extract_xyz() dih_proxies = get_complete_dihedral_proxies( pdb_hierarchy=pdb_h) for p in dih_proxies: for i_seq in p.i_seqs: print pdb_h.atoms()[i_seq].id_str(), print "angle=", dihedral_angle( sites=[sites_cart[x] for x in p.i_seqs], deg=True) print "Total angles:", dih_proxies.size()

def run(args): basics() advanced(args) all_dihedral_proxies(args)

if (__name__ == "__main__"): run(sys.argv[1:])

On Sun, Sep 20, 2015 at 3:30 PM, Nicholas Pearce < [email protected]> wrote:

...

Hi Everyone,

Phenomenally stupid question, but is there an easy way to calculate phi-psi angles for a protein using cctbx? And, following on from that, Chi-1, Chi-2 etc angles?

I’ve had a poke around, but couldn’t find any obvious (at least to me) way that worked…

I presume this must be implemented rigorously somewhere, and I didn’t want to waste time reimplementing the wheel.

Thanks, Nick _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb