[Chimera-users] Fitmap on overlap/correlation only within bounds of smallest map

[Oliver Clarke]

Hi,

I am trying to fit a set of large (whole protein) maps to a map corresponding to a single domain of the protein (extracted using ‘vop zone minimalbounds true’ with an atomic model of the domain in question.

It works fine, except that it takes rather a long time (~2000 steps), and the final correlation is 0.33, which is strange because the overall correlation between the two complete maps is ~0.95, and I can see that the final overlap between the aligned maps is good. 

It seems like ‘fitmap’ is calculating the correlation/overlap based on all grid points in the map that I am aligning, which has a much larger box size than the map to which I am aligning it. Is there any way to restrict the metric analysis to just consider points within the smaller box of the reference map? I cannot find such an option in the documentation for fitmap. 

The use case for this is when one has multiple conformations of a protein (for example, EM volumes after 3D-classsification) and would like to align them on a single reference domain.

Best,
Oliver.