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
