Hello, If you had a set of input files (say multiple .mrc files or multiple .pdb files), you could use the "forEachFile" option of the "open" command to run a ChimeraX command script (.cxc) on each one and derive the output names from the input names, as explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> However, I don't think this mechanism generalizes to a list of EMDB IDs instead of input data files. Your situation may require a different kind of script (shell? python?) -- which is beyond my skill set, so others would need to advise. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 12, 2022, at 10:03 AM, Nebojsa Bogdanovic via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I have a text file list of 30-40 maps from emdb that I would like to download and save using chimeraX. Each map should be named for example 5995.mrc, where 5995 is the actual EMDB id. Is there a way to do this using CLI to make it faster than downloading 1 by 1? I am not sure how to instruct chimeraX to take the file name from the open models.
open 5995 from emdb #opens the file and assigns #1 save ???.mrc models #1 #save the model 1 but how to instruct chimerax to take the model's name
Ideally would be something like this:
Input: emdb-ID.txt Output: 40 single .mrc maps named according to their EMDBIDs.
open emdb-ID.txt from emdb save all, models #1-40 name=????
Please let me know if I can implement this.
Thank you and best regards,
Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University