[Chimera-users] Fit to segments

[Luca Pellegrini]

Hi,

I am using ‘Fit to Segments’ to fit a crystal structure into the appropriate segment of an 18A EM map of a larger protein complex. The structure is one subunit of the complex. 

After initial manual alignment of the structure, fitting to the selected segment works well and produces what I believe is the correct orientation of the structure in the map. However, the fitting stats (Corr/At. Incl.) for the wrong hits are almost as good (within a few percent points), even though for some of them the structure is clearly misplaced in the segment. 

Can anyone please comment/advise on this? It looks like fitting and relative statistics are calculated relative to the entire map rather than the selected segment. I am using Chimera 1.10.1, build 40415.

Best wishes,
Luca

Luca Pellegrini
Department of Biochemistry
University of Cambridge
80 Tennis Court Road
Cambridge CB2 1GA
UK

Email: lp212 at cam.ac.uk
Phone: 0044-1223-760469