[Chimera-users] Fitting pdb model into difference map

Elaine Meng meng at cgl.ucsf.edu
Mon Apr 6 15:43:55 PDT 2015

Hello CE,
It may be the problem discussed earlier of differences between the two programs in handling the map origin, see:


So it may be a matter of changing the origin index in Chimera as described in that post.

However, if you are starting from scratch to do the fitting in Chimera, note that the "Fit in Map" GUI does only a local optimization and you would have to place the structure in a reasonable starting location.  If it is very far away, nothing will happen.  So you could try either manually moving the structure to a reasonable starting position...

… and/or using the "fitmap" command, which has some global search options.

I'd probably try the manual way first.  I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 6, 2015, at 1:48 PM, Chinaza Egbuta <egbutac at upstate.edu> 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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