pymol-users

[PyMOL] unable to change phi angle of proline

[Osvaldo M. <alo...@gm...>]

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.

Re: [PyMOL] unable to change phi angle of proline

[Thomas H. <sp...@us...>]

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 <alo...@gm...> 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.

Re: [PyMOL] unable to change phi angle of proline

[Osvaldo M. <alo...@gm...>]

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 <sp...@us...
> 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 <alo...@gm...> 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.
>
>