Re: [PyMOL] Finding the surface residues using code

2016-06-28 Thread Julian Heinrich
Dear Leila,

you can download the respective script using the link shown on the top
right of the wiki page:
https://github.com/Pymol-Scripts/Pymol-script-repo/raw/master/findSurfaceResidues.py

Run this script in PyMOL by invoking 'run findSurfaceResidues.py' (using
the path you downloaded the script to).
Then you can run the functions explained on the wiki page.

Cheers,
Julian

On Mon, Jun 27, 2016 at 9:58 AM leila karami 
wrote:

> Dear Pymol users,
>
> I am using Pymol v 1.7.x. I want to obtain and show the surface residues
> in my protein.
>
> I found the following link:
>
> http://www.pymolwiki.org/index.php/FindSurfaceResidues#Usage
>
> How to run the code being in this link?
>
> Best,
>
> --
> Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
> present their vision of the future. This family event has something for
> everyone, including kids. Get more information and register today.
> http://sdm.link/attshape___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] Transfer of the selection from reference to the ensemble

2016-06-28 Thread James Starlight
Dear Pymol Users!

Within the Pymol session I have 2 loaded superimposed objects:
1) one experimental pdb consisted of protein with cofactors (ligand and metals);
2) ensemble of 20 md snapshots of the same proteins superimposed on
each others without any cofactors;

For my particular task  I need
1) to copy the selection (which include metals and ligand atoms) from
the reference structure to each model of the MD ensemble (via Pymol),
2) make quick geometrical optimization of side-chains (I guess it
better to do it using Chimera) within the active side of each model
from MD ensemble
3) perform post-processing - analysis of the distances between
cofactors and optimized side-chains of each MD conformers to obtain
statistical distribution of averaged distances (I guess it better to
do it via some MD software like Gromacs).

I will be very thankful for any suggestions for practical realization
of those steps!



James

--
Attend Shape: An AT Tech Expo July 15-16. Meet us at AT Park in San
Francisco, CA to explore cutting-edge tech and listen to tech luminaries
present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net