Hi Saif, Can you please show us the commands you used in PyMOL to load the data and generate the map? (Also, can you send me a copy of the map and structure?) Has anyone else seen this problem?
I've looked over a few CCP4 maps in PyMOL, Maestro, and Coot side-by-side, and at various contours, they all look virtually identical. There are slight differences, probably due to algorithmic deviations, but they look good to me. In PyMOL: # mimic Coot set orthoscopic set line_width, 5 # get the data fetch 1cll, async=0 fetch 1cll, type=2fofc, async=0 # create the map; carve 2.5 Ang from the polymer isomesh 1cll_map,1cll_2fofc, 1.06, poly, carve=2.5 # find example residue orient i. 78 # color color magenta, e. N color tv_yellow, e. C In Coot: * Fetch 1CLL and its map from EDS * zoom to residue 78 * scroll to 1.06 sigma What do you see here? Cheers, -- Jason On Tue, Oct 26, 2010 at 9:50 AM, S. Saif Hasan <ssha...@purdue.edu> wrote: > Hello, > > I am trying to carve a 2Fo-Fc map around a lipid molecule. The electron > density > at 2 sigma is much smaller in PyMol than in Coot (the map at 1 sigma in PyMol > is similar to the 2 sigma level map in Coot). I used the "unset > normalize_ccp4_maps" command but that stops the carved map from being > generated. What should I do to solve this problem ? > > Thank you. > -- > Saif Hasan > > > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ 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
