[Chimera-users] Fitting pdb model into difference map

Tom Goddard goddard at sonic.net
Mon Apr 13 16:45:59 PDT 2015


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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