Hi Neena,
If you give a different selection, then phi_psi will give you a list of phi/psi
angles for all residues in the selection.
For example if your protein object is called "obj_1", then typing
phi_psi obj_1
will provide a list of phi_psi values to the terminal:
PyMOL>phi_psi obj_1
LYS-3: ( -63.3, -75.6 )
GLY-4: ( -62.6, -32.9 )
GLU-5: ( -31.7, -58.7 )
GLU-6: ( -57.3, -23.4 )
LEU-7: ( -74.7, -18.6 )
PHE-8: ( -106.0, 6.4 )
THR-9: ( -59.8, -16.1 )
GLY-10: ( -140.4, -166.5 )
or you can assign the list to a dictionary variable with:
p = cmd.phi_psi('obj_1')
where p will be a dictionary with keys representing the residue numbers and
pointing to a list of the phi/psi values for that residue.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Assistant Professor, Dept. of Biomedical & Molecular Sciences,
Queen's University, Kingston, ON K7L 3N6 Canada
<[email protected]> http://pldserver1.biochem.queensu.ca/~rlc
On Sat, 2020-05-09 11:08 -0400, Neena Susan Eappen <[email protected]>
wrote:
> Hi Jarrett,
>
> Thank you for your reply. However, that command gives phi and psi
> angles for only one atom (when only one atom is selected). Is there
> one command we can use to extract all phi and psi angles?
>
> Thanks,
> Neena
>
>
>
> On Mon, 27 Apr 2020 at 22:01, Jarrett Johnson <
> [email protected]> wrote:
>
> > Hi Neena,
> >
> > Is this command sufficient?
> >
> > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpymol.org%2Fdokuwiki%2Fdoku.php%3Fid%3Dcommand%3Aphi_psi&data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&sdata=Y8U07iXlCYJ%2BE0GN2Oh04QSE7n68NPH5d2fc%2BaUhdSk%3D&reserved=0
> >
> > Best,
> > Jarrett J
> >
> > On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <
> > [email protected]> wrote:
> >
> >> Hello PyMOL users,
> >>
> >> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
> >>
> >> Many thanks,
> >> Neena
> >> _______________________________________________
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> >>
> >
> >
> >
> > --
> >
> > *Jarrett Johnson* | Senior Developer
> > [image: Schrodinger Logo]
> > <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.schrodinger.com%2F&data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&sdata=QViEhtZ0MwQ2h0DLrVEcSdR%2FBW5DNGRF7kWbSDQIAaM%3D&reserved=0>
> >
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