[Chimera-users] Visulaizing maps from COOT in Chimera

Tom Goddard goddard at sonic.net
Tue Jul 5 10:23:49 PDT 2016

Hi Cedric,

  Chimera does not automatically extend maps by crystal symmetry like Coot (Chimera is primarily used for electron microscopy maps).  If your x-ray map is a unit cell you can use Chimera command

	vop cover #1 atom #2

where #1 is the model id of the map, and #2 is the model id of the atomic model.  If the map is just an asymmetric unit and not a full unit cell then Chimera will have to use space group symmetry to extend the map.  It can only do that if the space group symmetries are in the *.map CCP4 file.  You can see if those symmetries are present by using

	vol #0 dumpHeader true

and looking for the symop header value in the displayed output.  Coot can probably produce the space group symmetries from just the space group number (ispg header value), but Chimera does not do that.


> On Jul 4, 2016, at 6:11 AM, Cedric Govaerts <cgovaert at ulb.ac.be> wrote:
> Hi all,
> I would like to use Chimera to show a 2FO-FC or FO-FC electron density map (actually a tiny part of it)  obtained from COOT (or directly from the refinement program).
> If I open both the PDB file and the .map file, they are correctly open except that the bounding box from chimera truncate the map way to early.
> That's because my PDB absolute coordinate sit in the origin and it seem I cannot use negative value for the boundaries of the volume/map.
> How can I get the map to extend entirely over my protein ?
> Thanks !
> Cedric
> -- 
> Cedric Govaerts, Ph.D.
> Universite Libre de Bruxelles
> Campus Plaine. Phone :+32 2 650 53 77
> Building BC, Room 1C4 203
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> 1050 Brussels
> Belgium<lmhhpkhmepadlnpa.png>
> http://govaertslab.ulb.ac.be/ <http://govaertslab.ulb.ac.be/>_______________________________________________
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