How to sequentially open PDB files using a "for loop" in the UCSF chimera's command line?
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
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@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
Thanks a lot! On Thu, Sep 16, 2021 at 9:39 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
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#...
< 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@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
-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016
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