reporting sigma values for electron density maps
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 ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen@caltech.edu **********************************************
Hi David, The Tools menu in Volume Viewer includes "Volume Mean, SD, RMS" to report statistics for the current set of data. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/ volstats.html You probably want to make sure the whole map is displayed with step size 1 beforehand. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 20, 2008, at 2:43 PM, 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
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
participants (3)
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David Chenoweth -
Elaine Meng -
Tom Goddard