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 <nicholas.pearce@stx.ox.ac.uk> 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
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