[Chimera-users] Visulaizing maps from COOT in Chimera

Elaine Meng meng at cgl.ucsf.edu
Tue Jul 5 10:21:04 PDT 2016


I’d previously replied off-list, answer paraphrased here:

It may be necessary to use command “vop cover” as explained in this previous message:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-April/012166.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>

Some recent posts from Oliver regarding Chimera and Coot may also be useful:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-May/012313.html>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012392.html>

Elaine

> 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
> Boulevard du Triomphe, Acces 2
> 1050 Brussels
> Belgium
> <lmhhpkhmepadlnpa.png>
> http://govaertslab.ulb.ac.be/
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