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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