Hi Hongshi, I think Dale is right. When you turn off the normalization, the level value you need to put in the isomesh command should be the absolute electron density value of the map instead of how many RMSD.
In your command window log, this line shows the range of the density values in your map: ObjectMap: Map read. Range: -0.511 to 0.616 As you can see the highest value is 0.616, no wonder you see nothing when you tell the program to cut off at 3.0. And the line above it shows the RMSD, marked as stdev: ObjectMapCCP4: Current mean = -0.000066 and stdev = 0.074981. So for RMSD=3.0, the density cut off of this map is 0.075x3.0=0.225. Your command then is: isomesh fo-fc_ligand, bdligand002, 0.225 Or you can look at the coot window to find out what the density cut off is being used (map level=x.xxxx e/A^3 ), if you are not too sure about the RMSD calculation. An additional note: the same applies to UCSF Chimera, where the volume data (maps) control also requires you to specify the cut off or gradient in real map values instead of RMSD. Zhijie From: hongshi WANG Sent: Wednesday, February 19, 2014 3:47 PM To: Zhijie Li Subject: Re: [ccp4bb] Can not see density map when I turn off normalization in PYMOL Hi Zhijie, Thanks for your help. Once i turned off the normalization in pymol. I could not see any density map. hongshi On Wed, Feb 19, 2014 at 11:21 AM, Zhijie Li <zhijie...@utoronto.ca> wrote: Hi Hongshi, If you just put isomesh fo-fc_ligand, omitmap, 3 do you seem anything in the unit cell? If you do then please check if around your ligand there is any density. Zhijie From: hongshi WANG Sent: Wednesday, February 19, 2014 12:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Can not see density map when I turn off normalization in PYMOL 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
