Hello Flip, (1) we would generally recommend using ChimeraX over Chimera for many reasons: performance, enhanced features, current development and support. The rest of this answer applies to ChimeraX so I'm putting it on the chimerax-users list. (2) you can create a blank cubic grid first with "volume new" and then refer to that in the "molmap" command "onGrid" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> (3) I do not understand what you mean by losing secondary structure information when saving a map. Only atomic structures (not maps) have secondary structure information, i.e. helix and strand assignments. Can you clarify? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 6, 2024, at 10:40 AM, Flip Jansen via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hello Chimera dev team,

I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps.

One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map.

Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC?

Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information?

Any help is highly appreciated, I would also be happy to come by an talk in person.

Best, Flip Jansen