[Chimera-users] fit correlation

hsosa at aecom.yu.edu hsosa at aecom.yu.edu
Tue Jun 3 06:34:13 PDT 2008

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.



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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Hernando Sosa
Dept. of Physiology and Biophysics
Albert Einstein College of Medicine
1300 Morris Park Av.
Bronx NY 10461
phone	(718) 430-3456
FAX	(718) 430-8819
email	hsosa at aecom.yu.edu

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