[Chimera-users] Visulaizing maps from COOT in Chimera
cgovaert at ulb.ac.be
Tue Jul 5 13:10:39 PDT 2016
Thanks a lot Tom.
The vop cover command works great.
The dumpHeader is not a recognized keyword though.
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.
>> 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 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
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription:
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
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