Thank you very much Elaine. Have a good day George
On 18 Jan 2026, at 17:03, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi George, If you have a set of commands that work for each one, then you could put those commands into a command file (plain text file named something.cxc). These commands would need to include some option to save your results into file, for example, after you select the residues, to write the selection to a file using the "info residues sel" with "saveFile" option, or if you were using the "contacts" command to find the residues, that command also has a "saveFile". See the help pages for those commands, or whichever one(s) you are using. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues>
Instead of the specific output filename, in your cxc file you would include "$file" as part of the output filename so that it can be substituted differently for the multiple outputs from the multiple structures (otherwise it would overwrite and you would only get the last one).
Then you would need to put all your Boltz output complexes (PDB or CIF) in the same folder and then use the "open" command to open your .cxc file and specify with the "foreach" option (of the open command) the folder with the Boltz output complex files.
See "open" command option "forEachFile" for more details and an example: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile>
See ChimeraX command files: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-... <mhttps://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files>>
I hope this helps, Elained ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 18, 2026, at 8:35 AM, George Tzotzos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I’ve used the ChimeraX Boltz interface and obtained multiple models of the same ligand bound on to the same receptor. I’d like to find residues within 5A of the ligand. Of course, I can do this one at a time. I wonder if there’s a way to automate the process. Your help is much appreciated George
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