[Chimera-users] fit correlation

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jun 2 14:47:07 PDT 2008

Hi Elena,

   Cross correlation coefficients are frequently used to describe the 
quality of fit of an atomic model in an EM map.  Other measures such as 
the number of atoms at positions with density above 1 sigma are also used.

   The Chimera fit in map tool in recent Chimera versions (snapshot or 
daily build since Feb 20, 2008) can report correlation coefficient. 
Correlation measures the agreement between a simulated map at a 
specified resolution with the experimental map.  You enter that 
resolution in the fit map dialog in the options panel.  Also turn on 
"use map simulated from atoms".  Then press the "Update" button on the 
line of the dialog that says "correlation" and "average map value".

   The fitting also reports the number of atoms lying outside the 
displayed map contour surface.  You can set that to 1 sigma or 2 sigma 
or a value of your choosing.  To figure out the standard deviation of 
the map values use volume dialog menu Tools / Volume Mean, SD, RMS.

   More fit map documentation is in the manual


The volume guide also has info but is not up to date with the latest 
Chimera features:



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