[Chimera-users] Visulaizing maps from COOT in Chimera

Oliver Clarke olibclarke at gmail.com
Tue Jul 5 10:25:08 PDT 2016


Hi Cedric,

Chimera cannot extend the map to cover your molecule - it does not have the symmetry expansion features available in coot. I have an extension for Coot (available as part of this script: https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0) which will open the region of the map(s) currently displayed in coot in Chimera, perhaps this will be useful for you. 

Alternatively, when you are calculating the map, make sure you calculate it to cover your entire molecule (there are options in both phenix and refmac for this purpose).

Cheers,
Oli.
> Date: Mon, 4 Jul 2016 15:11:56 +0200
> From: Cedric Govaerts <cgovaert at ulb.ac.be>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Visulaizing maps from COOT in Chimera
> Message-ID: <6db1dd6b-2fc9-9fd9-158c-34db965d5a8f at ulb.ac.be>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
> 
> 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
> http://govaertslab.ulb.ac.be/
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