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.htm...
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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- ----------------------------------- 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@aecom.yu.edu -----------------------------------