When you don't normalize the map you have to specify your contour level in whatever units the map came in. Your output says the "stdev" is 0.075 so I guess you need to contour at 0.225 to see the equivalent image.
Dale Tronrud P.S. I feel compelled to note that what the program is reporting as the "standard deviation" is really the root mean square deviation from zero. The standard deviation of a map is a much more subtle quantity as discussed recently in PNAS. On 02/19/2014 09:30 AM, hongshi WANG wrote: > Hello there, > > > > I am making a fo-fc map for one ligand using pymol. I strictly followed > the pymol wiki protocol (Display CCP4 Maps). Finally, I can get the > ligand map using command: > > isomesh fo-fc_ligand, omitmap, 3, ligand, carve=2. > > However, the problem is the map I got from pymol is smaller than the one > I can see in coot at the same contour level (3.0). > > So I gave a second trial based on the assumption that it may be caused > by the mis-normalization. I input the command: “unset > normalize_ccp4_maps” to stop PyMOL from normalizing a cpp4 map. After > that I loaded my ccp4 map file and tried to do the same things as what I > did for the first time. But I could not see any mesh net (density map) > shown up. I check the command window. > > /PyMOL>unset normalize_ccp4_maps/ > > / Setting: normalize_ccp4_maps set to off./ > > / ObjectMapCCP4: Map Size 134 x 128 x 122/ > > / ObjectMapCCP4: Map will not be normalized./ > > / ObjectMapCCP4: Current mean = -0.000066 and stdev = 0.074981./ > > / ObjectMap: Map read. Range: -0.511 to 0.616/ > > / Crystal: Unit Cell 200 300 100/ > > / Crystal: Alpha Beta Gamma 90.000 100.354 90.000/ > > / Crystal: RealToFrac Matrix/ > > / Crystal: 0.0060 -0.0000 0.0011/ > > / Crystal: 0.0000 0.0045 -0.0000/ > > / Crystal: 0.0000 0.0000 0.0053/ > > / Crystal: FracToReal Matrix/ > > / Crystal: 200 0.0000 -34.5817/ > > / Crystal: 0.0000 300 0.0000/ > > / Crystal: 0.0000 0.0000 100/ > > / Crystal: Unit Cell Volume 6993536./ > > / ExecutiveLoad: "E:/ bdligand002.ccp4" loaded as "bdligand002", through > state 1./ > > / PyMOL>isomesh fo-fc_ligand, bdligand002, 3, ligand, carve=2/ > > / Executive: object "fo-fc_ligand" created./ > > / Isomesh: created "fo-fc_ligand", setting level to 2/ > > / ObjectMesh: updating "fo-fc_ligand"./ > > > > It seems like no error, but my ligand map, fo-fc_ligand has no density > map shown up. I also tried to show the whole mesh at level 2.0 for > bdligand002. I still could not see the density map. > > > > My pymol is version 1.3 in windows 8 operation system. > > > > > > Any help will be greatly appreciated! > > > > Thanks in advance > > > > hongshi >
