[Chimera-users] how to save molmap by command line

[Elaine Meng]

Dear Guido,
The Chimera "save" command is for saving sessions.

In Chimera, the command to save map files is "volume" with option "save <filename>" ... you need to specify map model number, and there are several other options that could be used, see:

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>

Example:

volume #3 save ~/Desktop/test.mrc

Note that in ChimeraX (a different program than Chimera) you can use the "save" command to save maps and several other kinds of files.

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


> On Jan 23, 2023, at 1:06 AM, Guido Leoni via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear list 
> I would use in programmatic way chimera to elaborate a molmap of a peptide bound in a receptor. 
> I'm able to load the pdb and elaborate the molmap of the peptide
> 
> "/home/guido/.local/UCSF-Chimera64-1.16/bin/chimera --nogui load <NAMEFILE>
> molmap :.P 5;"
> 
> Now I would save the molmap of the peptide to do a fitmap vs another peptide.
> I tried 
> save test.mrc
> 
> but the following msg is prompted to me 
> Volume data sets
> 
> molmap <namefile>.pdb res 5
> 
> were not saved in the session.  To have them included
> in the session they must be saved in separate volume
> files before the session is saved.
> 
> DO you have any tips?
> 
> Thank you 
> Guido
> 
> 
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