Hello, Probably the better approach is to make a command file (.cxc) that works for a single example. Next you would modify the command file to contain "$file" instead of the specific filenames, and then open the command file using the "open" command with the "forEachFile" option. See the full explanation of how to do it, including an example, in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> I hope this helps, Elaine ----- 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 May 31, 2024, at 8:54 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX Users !

I am dealing with the analysis of multiple structural coordinates generated by AlphaFold for a target protein in *.cif extension. My goal is superimpose all the coordinates to the first model and save them in .pdb as separate files. So my script could be:

open ./*.cif match #2-6 to #1 # probably there is a better solution # and some command for save

What could be the solution to save all the coordinates in automatic way in separate pdb with the name patterns corresponded to the ID of these models ?

Many thanks in advance

Enrico

Brilliant, thank you very much Tom ! All the best Enrico Il giorno ven 31 mag 2024 alle ore 21:27 Tom Goddard <goddard@sonic.net> ha scritto:

Hi Enrico,

open *.cif matchmaker #2-5 to #1 save [NAME] format pdb models #1-5 relModel #1

or

save alphafold_[ID].pdb format pdb models #1-5 relModel #1

Please read the documentation before asking.

https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#pdb

Tom

On May 31, 2024, at 8:54 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX Users !

I am dealing with the analysis of multiple structural coordinates generated by AlphaFold for a target protein in *.cif extension. My goal is superimpose all the coordinates to the first model and save them in .pdb as separate files. So my script could be:

open ./*.cif match #2-6 to #1 # probably there is a better solution # and some command for save

What could be the solution to save all the coordinates in automatic way in separate pdb with the name patterns corresponded to the ID of these models ?

Many thanks in advance

Enrico _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/