[Chimera-users] Question regarding saving protein-ligand and docking in Chimera

[Tarazkar, Maryam]

Hi Elaine,
Thank you for getting back to me.
I went through your recommentation #3 and it worked for me.
The only thing is that looks like the first position of ligand (#2.1) is saved with PDB. So I saved in Mol2, but not sure if Mol2 save all configurations in single file?
So to analyze the docking results should I consider all 10 configurations? In principle I do not understand what does the 10 configurations, proposed in docking results, mean?
Best,
Maryam
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, September 2, 2020 4:13 PM
To: Tarazkar, Maryam <Maryam.Tarazkar at ucsf.edu>
Cc: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Question regarding saving protein-ligand and docking in Chimera

Dear Maryam,
You did not show the error so I don't know what happened.

(1)  Make sure you do not include model #3 ("search volume") because that is not an atomic model.  Also you probably do not want to include #0 because that is the ligand in the original undocked position.

(2) Make sure you have permission to write files in the location you are trying to save to.

(3) Pymol can open more than one file at the same time.  Why not just save docked positions of the ligand (#2) to one file  "relative to model" #1 which is the receptor.  The "relative to" option will make sure they are in the right position when you open the receptor from a separate file, which could be the same PDB file that you originally opened in Chimera, Ebour.pdb.  I.e. in Pymol just open "Ebour.pdb" and then also open the PDB file of docked ligand positions that you saved from Chimera.  Also I don't know if Pymol likes it when you save multiple positions to one PDB file.  It might only show the first one instead of all of the positions.  In that case you might try saving the docked ligand positions as Mol2 from Chimera instead of as PDB.

(4) You may know that Chimera has a ViewDock tool for convenient analysis of the docking results.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html>

However, maybe you are more familiar with Pymol and want to use it instead, which is fine, but  as I mentioned above, I don't know what kind of input is best for the docking analysis in that program and I can't give detailed advice.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 2, 2020, at 3:35 PM, Tarazkar, Maryam <Maryam.Tarazkar at ucsf.edu> wrote:
>
> Dear Sir or Madam,
> I did molecular docking to find the protein-ligand interactions using Chimera. Now I am trying to save the results of docking ( I took the screenshot here) in a text file and save the structure of protein-ligand in pdb file so I do the analysis using Pymol.
> When I click on file--> save pdb a page appears where I have to select which models to be saved.
> ( I took the screenshot of the page here) but when I select ligand, protein and docked options all tigetehr, the program gives me error in saving the files.
> I appreciate if you help me and let me know how I can resolve it and save the protein-ligand structure in best binding site in pdb so I do further analysis on this.
> Best
> Maryam
> <image.png>
> <image.png>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200904/2031a731/attachment-0001.html>