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
 

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DeLano Scientific LLC
Subscriber Support Services
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From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@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