Dear Hongshi - I cant help but to first suggest that as this is the CCP4bb, the first thing you should try is using CCP4mg, if you want to make pretty pictures. If you just want to look at the map and work with it, you should use Coot.
If still for some reason you want to use Pymol, you should ask the experts of Pymol, and its best to mail pymol-us...@lists.sourceforge.net These said, you do not specify what you really want to do. Is the ligand already there in the coordinates file? Then an fo-fc (difference) map should show you nothing, as the ligand is there and there should be no difference. If the ligands is not there in the coordinates file, and you see no density, then the ligand is simply not there. Hope these help, Tassos On 19 Feb 2014, at 18:30, 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 >
