[Chimera-users] Visulaizing maps from COOT in Chimera

[Cedric Govaerts]

Thanks a lot Tom.
The vop cover command works great.

The dumpHeader is not a recognized keyword though.

Cedric


On 5/07/2016 19:23, Tom Goddard wrote:
> 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.
>
> Tom
>
>
>
>> On Jul 4, 2016, at 6:11 AM, Cedric Govaerts <cgovaert at ulb.ac.be 
>> <mailto: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/
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu 
>> <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: 
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

-- 
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/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20160705/e2a7f7de/attachment.html>