[chimerax-users] downloading and saving maps from EMDB

[Elaine Meng]

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 at 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