On Jan 13, 2022, at 6:54 PM, Guan, Lan <Lan.Guan@ttuhsc.edu> wrote:
Dear Elaine,
I try to generate a reference model from crystal structure pdb file for cryo-EM particle alignment.
I can get the map by “molmap #1 6”; #1 = my pdb file id; 6 = resolution I want to get in the output model.
After imported into cryosparc, I can not use it. Error “ Cubic volumes only”. My question is how to change this Molmap output into a cubic volumes in Chimera? I would appreciate for your input.
Lan
Hi Lan, (CC'ing chimera-users@cgl.ucsf.edu which is the address recommended for asking questions since others may have better answers) I don't know what cryosparc means by "cubic volumes only". My only guess is that maybe you did not save the molmap map correctly. The molmap command should make a new model which is the map, and then you can save the map with the Volume Viewer tool's File menu, or with the "volume" command. Saving data: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html> Volume Viewer menu (File... Save map as...) <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu...> volume command saving options <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output> Or, maybe cryosparc does not read any of the map formats that Chimera can write (listed in the link above). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco