[Chimera-users] Question on pdb to mrc

[Elaine Meng]

> 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:
<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/volumeviewer.html#organization>

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