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