Here's some Python code you can open in ChimeraX to fetch EMDB maps and save them to MRC files.

# Fetch EMDB maps and save them to MRC files. ids = ['5995', '1080', '12555'] from chimerax.core.commands import run for id in ids: run(session, f'open {id} from emdb') run(session, f'save {id}.mrc') run(session, f'close')

Tom

On Jul 12, 2022, at 1:38 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

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

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Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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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

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