[Chimera-users] Saving mrc EM-map

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 6 11:07:50 PST 2018

Hi Ibraham,
In general, moving the map around in the view is not going to change the header.  (Also, map headers do not contain rotation information.)  This is explained in the bottom section of this page:


As mentioned in the next-to-last sentence on that page, to reposition the origin (no rotation, only translation) you can use the “Coordinates” section of Volume Viewer (show this section using Volume Viewer’s “Features” menu):

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

> On Dec 6, 2018, at 9:52 AM, Ibrahim M. Moustafa <ria2 at psu.edu> wrote:
> Hi All,
>   I'm trying to do the fitting of a model into EM (mrc map) for real-space-refine in phenix.
> First I read the map and clicked "center" in the Volume viewer. Then I saved the centered map, assuming that the header info will be updated in the saved map.
> I did the fitting and saved the model relative to the map. Reading the saved map and fitted model back looks OK. However, when I do the real-space-refine in Phenix, the CC-value during the run is really low (0.01) suggesting something is not properly done. I checked the header (using mrcfile) of the saved "centered" map and compared it to the original map and it is the same "0,0,0". Which means chimera did not update the header after centering.
>     I'm not if there is a more proper way to do this! Any advice?
>   Thank you for your help.
>   Ibrahim   
> Ibrahim M.Moustafa, Ph.D.
> Pennsylvania State University
> Biochemistry & Molecular Biology Dept.
> Millennium Science Complex
> University Park, PA16802
> Tel (814)863 5940
> Fax (814)865 7927
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