[Chimera-users] Fitting pdb model into difference map

Tom Goddard goddard at sonic.net
Mon Apr 13 16:58:25 PDT 2015


Actually Chimera can extend your difference map to cover the unit cell with this Chimera command

	vop cover #0 ibox 0,0,0,156,156,132

where #0 is your difference map.  The “vop cover” command extends a map by symmetry and the 0,0,0,156,156,132 argument is the grid indices to cover extending your map which is of size 156,156,23 to cover a full unit cell.  I didn’t think this would work, but in fact Chimera read the crystal symmetry operators from the CCP4 map file and it worked on the map you sent me.

	http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/vop.html#cover

  Tom



> On Apr 13, 2015, at 4:45 PM, Tom Goddard  wrote:
> 
> Hi CE,
> 
>  Thanks for sending me your map and PDB model — they are correctly aligned.  The problem is that the map doesn’t cover the atomic model because the map contains only 1/6 of the full unit cell, and there are 6 crystallographic symmetry operators to extend the map to the full unit cell.  Coot knows how to extend the map using the crystallographic symmetry operators but Chimera does not.  To make the map overlap with the atomic model in Chimera you will need to compute a full unit cell map using other software.
> 
> 	Tom
> 
> 
>> On Apr 6, 2015, at 1:48 PM, Chinaza Egbuta wrote:
>> 
>> I generated an Fo-Fc difference map using CCP4i and was able to superimpose the PDB model structure onto the map in Coot but I am unable to do so with Chimera.  The model and map are offset/rotated away from each other and I have not been able to fit the model into the map with Volume Viewer --> Tools --> Fit in Map.  Please let me know how I can get around this issue.
>> 
>> Thank you.
>> 
>> CE
>> 
>> 
>> 
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