Set phipsi

From PyMOLWiki
Revision as of 03:23, 6 May 2013 by Speleo3 (talk | contribs) (usage+examples)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

Set phi/psi angles for all residues in selection.

Posted on pymol-users mailing list:


set_phipsi selection [, phi [, psi ]]

The Script

from pymol import cmd

def set_phipsi(selection, phi=None, psi=None):

    Set phi/psi angles for all residues in selection.


    set_phi, set_psi, set_dihedral, phi_psi, cmd.get_phipsi, DynoPlot
    for model, index in cmd.index('byca (' + selection + ')'):
        atsele = [
            'first ((%s`%d) extend 2 and name C)' % (model, index), # prev C
            'first ((%s`%d) extend 1 and name N)' % (model, index), # this N
            '(%s`%d)' % (model, index),                             # this CA
            'last ((%s`%d) extend 1 and name C)' % (model, index),  # this C
            'last ((%s`%d) extend 2 and name N)' % (model, index),  # next N
            if phi is not None:
                cmd.set_dihedral(atsele[0], atsele[1], atsele[2], atsele[3], phi)
            if psi is not None:
                cmd.set_dihedral(atsele[1], atsele[2], atsele[3], atsele[4], psi)
            print ' Error: cmd.set_dihedral failed'

def set_phi(selection, phi):
    set_phipsi(selection, phi=phi)

def set_psi(selection, psi):
    set_phipsi(selection, psi=psi)

cmd.extend('set_phipsi', set_phipsi)
cmd.extend('set_phi', set_phi)
cmd.extend('set_psi', set_psi)

# vi:expandtab:smarttab:sw=4


# load script

# make alpha helix
set_phipsi resi 5-20, -64, -41

# make beta sheet
set_phipsi resi 30-40, -120, 120

See Also