[Chimera-users] How to sequentially open PDB files using a "for loop" in the UCSF chimera's command line?

[Elaine Meng]

Hi Prathvi,
There is no "for loop" to process multiple PDB files using the Chimera command line.  Instead you would have to use Python as described here:
<https://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

However, you can do it in ChimeraX:  when opening a ChimeraX command file, you can use the ChimeraX command "open" with the "forEachFile" option to run it on multiple input files, e.g.

open myscript.cxc foreach  ~/mypdbfolder/*.pdb

<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>
<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile>

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

> On Sep 16, 2021, at 12:21 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Greetings,
> Is it possible to use a "for loop" in the UCSF chimera's command line to open a PDB file, perform an action (say delete an atom), save the PDB file & close it, open the next PDB file, perform the same operation, save it & close it and so on.
> Thanks,
> Prathvi