[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.
http://www.cgl.ucsf.edu/chimera/plans.html
Tom
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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