Yes, that is the default behavior for PyMOL as well.
To disable it, issue:
before loading your map file.
DeLano Scientific LLC
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
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."
Does PyMOL also scale the average density to zero and the standard deviation to
The Department of Biochemistry
and Molecular Biology
The Pennsylvania State