When you open your Fo-Fc map and the PDB model in Coot they automatically align right? They should also automatically align in Chimera provided you read the map in with the right file type (CCP4, file suffix .ccp4 or .map). If you read the map in as MRC format then you might get misalignment because that will use a different header value in the map file for the origin used for electron microscopy data. The Chimera Fit in Map tool isn’t going to correctly fit a molecule in an Fo-Fc difference map since that map shows the errors (amplitudes observed in x-ray experiment minus amplitudes calculated for the current best guess at the atomic model). Chimera has no tools for fitting using a difference map that represents the errors in a fit. 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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