Mike, Yes, that is the default behavior for PyMOL as well. To disable it, issue: unset normalize_ccp4_maps before loading your map file. Cheers, Warren
-- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com _____ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of MIKE GLEGHORN Sent: Wednesday, July 16, 2008 7:42 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] .ccp4 map normalization - what does it mean? Hello, At http://pymol.sourceforge.net/faq.html it says that "...PyMOL now reads and normalizes CCP4 maps on the fly!" and mentions xdlmapman and mapman as alternatives. For xdlmapman at http://www.ccp4.ac.uk/html/xdlmapman.html it says "The map will be scaled such that the average density is zero and the standard deviation ("sigma") is one." For mapman at http://xray.bmc.uu.se/usf/ it says "gives a map an average value of zero and a standard deviation of one by first subtracting the average and then dividing by the old standard deviation." My question: Does PyMOL also scale the average density to zero and the standard deviation to one? Mike Gleghorn Graduate Student The Department of Biochemistry and Molecular Biology The Pennsylvania State University
