Thanks Thomas,
I tried your solution (adapted to my code) and now everything is working.
def set_phi(res_num, res_name, phi):
if res_num != 0 and res_name != 'PRO':
cmd.set_dihedral('resi %s and name C' % (res_num-1), 'resi %s and
name N' % res_num, 'resi %s and name CA' % res_num, 'resi %s and name C' %
res_num, phi, state=1, quiet=1)
if res_num != 0 and res_name == 'PRO':
cmd.unbond('resi %s and name N' % res_num, 'resi %s and name CD' %
res_num)
cmd.set_dihedral('resi %s and name C' % (res_num-1), 'resi %s and
name N' % res_num, 'resi %s and name CA' % res_num, 'resi %s and name C' %
res_num, phi, state=1, quiet=1)
cmd.bond('resi %s and name N' % res_num, 'resi %s and name CD' %
res_num
Cheers,
Osvaldo.
On Fri, Oct 4, 2013 at 9:50 AM, Thomas Holder <[email protected]
> wrote:
> Hi Osvaldo,
>
> unfortunately PyMOL doesn't handle to set dihedrals in rings, so you have
> to break the ring first. Consider this:
>
> def set_phi(resi, phi, state=1, quiet=1):
> x = cmd.index('(first (resi %s and guide)) extend 2 and name C+N+CA' %
> resi)
> try:
> a = cmd.get_model(x[2], state).atom[0]
> if a.name != "CA":
> raise IndexError
> except IndexError:
> print " missing atoms"
> return
> if a.resn == "PRO":
> bondargs = (x[1], "resi %s and name CD" % resi)
> cmd.unbond(*bondargs)
> cmd.set_dihedral(x[0], x[1], x[2], x[3], phi, state, quiet)
> if a.resn == "PRO":
> cmd.bond(*bondargs)
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> On Oct 2, 2013, at 8:28 PM, Osvaldo Martin <[email protected]> wrote:
> > Hi everybody,
> >
> > I can´t change the phi angle of proline using the function below. It
> works for all other amino acids. If quiet = 0, it prints the value of the
> variable "phi" (i.e. the value that the phi_angle should adopt). The phi
> angle of proline is always around ~11.0
> >
> > def set_phi(res_num, phi):
> > if res_num != 0:
> > cmd.set_dihedral('resi %s and name C' % (res_num-1), 'resi %s
> and name N' % res_num, 'resi %s and name CA' % res_num, 'resi %s and name
> C' % res_num, phi, state=1, quiet=1)
> >
> > Thanks in advance.
>
>
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