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@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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