[Chimera-users] EM density map rescaling issue???

Tom Goddard goddard at sonic.net
Tue May 13 10:53:18 PDT 2014

Hi Christian,

  Set the “voxel size” in the Coordinates panel of the Chimera Volume Viewer dialog (menu Features / Coordinates) to 8.6.  The Tomography Toolbox format *.em does include a voxel size value and Chimera reads it but apparently it is not set or it is set to 1 Angstrom in your map file.  If you save your map as say MRC it will have the new voxel size.  Or if you save a Chimera session it will have the new voxel size.  Chimera does not write Tomography Toolbox format so it cannot rewrite that file.


On May 13, 2014, at 2:06 AM, Christian Geiss wrote:

> Dear Chimera User list,
> I have a fundamental problem when loading pdb structures and EM density maps as *.em. The scale doesn't fit at all, with other words my pdb structure
> is tremendously bigger than the EM structure. One work-around is to resample the EM structure from current 64 px boxsize with 8.6 A pixelsize to 1 A pixelsize, giving
> ~ a 500 pixel volume, but then the volume gets quite big und my chimera gets really slow in handling those structures (pdb and big EM map at once)...is there any other way to solve this issue like scaling the EM structure on the fly in not such a memory consuming way...I also wonder if there is any information about the pixelsize in the EM header, because then the scaling should be done usually automatically???
> Thanks in advance,
> Chris
> P.S. I couldn't find anything related to this in the chimera archive...
> -- 
> Christian Geiss, M.sc.
> Universitaet Frankfurt BMLS
> Frangakis Group
> Max-von-Laue-Strasse 15
> D - 60438 Frankfurt am Main
> Phone: +49-(0)69-79842597
> Fax: +49-(0)69-79846467
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140513/1432ca0b/attachment.html>

More information about the Chimera-users mailing list