[Chimera-users] multiple structures to minimize

[Elaine Meng]

> On Apr 19, 2018, at 5:21 AM, Lu Yang <luy at princeton.edu> wrote:
> 
> Hi Elaine,
> I’m a Chimera-user and have a question of structure minimization. I have multiple structures to minimize for ligand docking simulation. I wonder if I can open them all in chimera, and select all of them for structure minimization? Will they affect each other? Because otherwise I’ll have to go through open -> minimize -> wait -> save one by one. 
> Best,
> Ling
> -----------------------------------------------------------------------
> Lu (Ling) Yang
> Ph.D candidate | Andolfatto Lab
> Ecology & Evolutionary Biology | Princeton University
> www.luyangevolution.com
> 

Hi Ling,
It is recommended to send questions to chimera-users at cgl.ucsf.edu (CC’d here) to ensure getting an answer.

As it says in the “minimize structure” help page,
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>
"All chosen models are treated as a single system” which is not what you want.

It sounds like it would be better to write a script using Chimera’s “minimize” command.  First try this on one ligand structure by entering the command directly, to figure out what command options to use.  After you figure out the correct Chimera command, you can write a Python script to loop through multiple ligands, opening (“open” command), minimizing, and saving (“write” command) them one by one.  See documentation for individual commands and their options:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

… and for writing a Python script to loop through multiple structures:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

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