[Chimera-users] reporting sigma values for electron density maps

Tom Goddard goddard at cgl.ucsf.edu
Tue May 20 15:54:10 PDT 2008

Hi Dave,

  Chimera can report the mean, standard deviation and root mean square 
map value using menu entry

    Tools / Volume Data / Volume Mean, SD, RMS

The values using whatever normalization the map file has.  If you divide 
the threshold level you set in the volume dialog by the RMS value you 
will get a sigma value.  Actually I'm not sure if that is correct -- 
depends on the definition of sigma.  Maybe you have to take the volume 
dialog number, subtract the mean and divide by the SD.  The reported SD 
and RMS differ only in that the SD is the standard deviation of the map 
about the mean while the RMS is the standard deviation about 0.

  Allowing the volume dialog to show the sigma values directly is on our 
requested features list (item 88) but has not yet been implemented.



David Chenoweth wrote:
> Hi!
> Can you please let me know if there is a way to report or set the  
> sigma value for an electron density map from a high resolution crystal  
> structure. I am using a ccp4 FWT.map and DELFWT.map file for  
> structures <1.2 angstrom resolution. Can I somehow find the sigma  
> value that corresponds to the Level setting in the Volume viewer?
> Thanks,
> Dave Chenoweth

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