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