[Chimera-users] Question on pdb to mrc

Elaine Meng meng at cgl.ucsf.edu
Fri Jan 14 08:49:54 PST 2022

> On Jan 13, 2022, at 6:54 PM, Guan, Lan <Lan.Guan at 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 at 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:

Volume Viewer menu (File... Save map as...)

volume command saving options

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 C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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