pymol-users

[PyMOL] Extract all phi and psi angles

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

How to extract all peptide dihedral angles (phi and psi) in PyMOL?

Many thanks,
Neena

Re: [PyMOL] Extract all phi and psi angles

[Jarrett J. <jar...@sc...>]

Hi Neena,

Is this command sufficient?

https://pymol.org/dokuwiki/doku.php?id=command:phi_psi

Best,
Jarrett J

On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <nee...@gm...>
wrote:

> Hello PyMOL users,
>
> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
>
> Many thanks,
> Neena
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

Re: [PyMOL] Extract all phi and psi angles

[Neena S. E. <nee...@gm...>]

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 <
jar...@sc...> wrote:

> Hi Neena,
>
> Is this command sufficient?
>
> https://pymol.org/dokuwiki/doku.php?id=command:phi_psi
>
> Best,
> Jarrett J
>
> On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <
> nee...@gm...> wrote:
>
>> Hello PyMOL users,
>>
>> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
>>
>> Many thanks,
>> Neena
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
>
> *Jarrett Johnson* | Senior Developer
> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>

Re: [PyMOL] Extract all phi and psi angles

[Robert C. <rob...@qu...>]

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
<rob...@qu...>  http://pldserver1.biochem.queensu.ca/~rlc


On Sat, 2020-05-09 11:08  -0400,  Neena Susan Eappen <nee...@gm...> 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 <
> jar...@sc...> 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&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&amp;sdata=Y8U07iXlCYJ%2BE0GN2Oh04QSE7n68NPH5d2fc%2BaUhdSk%3D&amp;reserved=0
> >
> > Best,
> > Jarrett J
> >
> > On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <  
> > nee...@gm...> wrote:  
> >  
> >> Hello PyMOL users,
> >>
> >> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
> >>
> >> Many thanks,
> >> Neena
> >> _______________________________________________
> >> PyMOL-users mailing list
> >> Archives:
> >> https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&amp;sdata=%2F%2F%2BSyfR20FyqY2GFMhZVbBe0CHtQuoSLCIUMsBHgoLs%3D&amp;reserved=0
> >> Unsubscribe:
> >> https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&amp;sdata=gcqmQ9A%2BOEJMPVf3ubqWWGEh6DzZv95XVXXJULabe2w%3D&amp;reserved=0
> >>  
> >
> >
> >
> > --
> >
> > *Jarrett Johnson* | Senior Developer
> > [image: Schrodinger Logo]
> > <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.schrodinger.com%2F&amp;data=02%7C01%7Crobert.campbell%40queensu.ca%7C220f11d984f74518dfe208d7f42b243e%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C637246338451090438&amp;sdata=QViEhtZ0MwQ2h0DLrVEcSdR%2FBW5DNGRF7kWbSDQIAaM%3D&amp;reserved=0> 

Re: [PyMOL] Extract all phi and psi angles

[Tamas H. <bio...@gm...>]

Hi,

For this type of analysis I would use MDAnalysis (Python):
https://www.mdanalysis.org/
https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html

Tamas

On 5/9/20 5:08 PM, Neena Susan Eappen 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 
> <jar...@sc... 
> <mailto:jar...@sc...>> wrote:
>
>     Hi Neena,
>
>     Is this command sufficient?
>
>     https://pymol.org/dokuwiki/doku.php?id=command:phi_psi
>
>     Best,
>     Jarrett J
>
>     On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen
>     <nee...@gm... <mailto:nee...@gm...>> wrote:
>
>         Hello PyMOL users,
>
>         How to extract all peptide dihedral angles (phi and psi) in PyMOL?
>
>         Many thanks,
>         Neena
>         _______________________________________________
>         PyMOL-users mailing list
>         Archives:
>         http://www.mail-archive.com/pym...@li...
>         Unsubscribe:
>         https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
>     -- 
>
>     *Jarrett Johnson* | Senior Developer
>
>     Schrodinger Logo <https://www.schrodinger.com/>
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Extract all phi and psi angles

[Neena S. E. <nee...@gm...>]

Thank you Tamas, for suggesting that great MDanalysis tool, will try it
out!

Thank you Rob, yes that command worked (phi_psi obj), it gave a list of all
backbone dihedral angles!

On Sat, 9 May 2020 at 12:45, Tamas Hegedus <bio...@gm...> wrote:

> Hi,
>
> For this type of analysis I would use MDAnalysis (Python):
> https://www.mdanalysis.org/
>
> https://www.mdanalysis.org/mdanalysis/documentation_pages/analysis/dihedrals.html
>
> Tamas
>
> On 5/9/20 5:08 PM, Neena Susan Eappen 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 <
> jar...@sc...> wrote:
>
>> Hi Neena,
>>
>> Is this command sufficient?
>>
>> https://pymol.org/dokuwiki/doku.php?id=command:phi_psi
>>
>> Best,
>> Jarrett J
>>
>> On Mon, Apr 27, 2020 at 9:45 PM Neena Susan Eappen <
>> nee...@gm...> wrote:
>>
>>> Hello PyMOL users,
>>>
>>> How to extract all peptide dihedral angles (phi and psi) in PyMOL?
>>>
>>> Many thanks,
>>> Neena
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> Archives: http://www.mail-archive.com/pym...@li...
>>> Unsubscribe:
>>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>>
>>
>>
>> --
>>
>> *Jarrett Johnson* | Senior Developer
>> [image: Schrodinger Logo] <https://www.schrodinger.com/>
>>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe