Greetings Michael, I suspect this is a question PyMOL automatically normalizing the map values, whereas the other programs might not. For historical reasons, PyMOL's default behavior is to normalize CCP4 map values upon loading. To prevent this, issue:
unset normalize_ccp4_maps before loading the map file. Cheers, Warren > -----Original Message----- > From: Michael Oldham [mailto:mlold...@purdue.edu] > Sent: Monday, June 08, 2009 1:18 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] map smaller than in Coot > > I have a map that I generated from VOIDOO for a cavity in my protein > structure. In Coot and O it shows up as the same size and fully covers > a ligand visible in my structure. In PyMol it is visibly smaller and > does not cover the ligand as well. does anyone have any idea of a > parameter that can be changed to show the map as it looks in Coot. > > Thanks > > > ------------------------------------------------------------------------ -- > ---- > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
