[Chimera-users] fit correlation

Tom Goddard goddard at cgl.ucsf.edu
Tue Jun 3 13:19:51 PDT 2008

Hi Hernando,

  If the fit in map option to "Use only data above contour level from 
first map" is enabled (it is by default) then the correlation is 
calculated using only grid points within the displayed contour level of 
the first map.  If you turn that option off, then the correlation uses 
all grid points of the first map.  If the second map contains other 
structures (e.g. other asymmetric units) within the bounds of the first 
map box, then using all grid points will give a lower correlation due to 
the mismatch between the maps in those regions.  So it is usually best 
to use the default setting and set the contour level of the first map 
low enough to include all grid points where the correlation is desired.


hsosa at aecom.yu.edu wrote:
> One thing I am curious about it,  when calculating correlation values, 
> is how to deal with cases in which the pdb atomic structure of only 
> one asymmetric unit is fitted into an electron density corresponding 
> to more than one asymmetric unit.  Is there an easy way to exclude 
> from the calculation  the densities corresponding  to the extra 
> asymmetric units.
> Thanks
> Hernando
> Thomas Goddard wrote:
>> 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
>>     http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html 
>> The volume guide also has info but is not up to date with the latest 
>> Chimera features:
>>     http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmap 
>>    Tom
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