Re: [ccp4bb] Displaying electron density in PYMOL

[Roger Rowlett]

How are you creating your map for Pymol? You can find instructions for constructing sensible omit maps using refmac5 and fft in CCP4 here: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Building+and+Validation#Creating_Omit_Maps_for_Ligands_using_Refmac For displaying omit maps in Pymol look here: http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Visualization+of+PDB+files#Visualizing_Electron_Density_Maps Cheers, Roger Rowlett On 2/10/2010 3:16 PM, Raja Dey wrote: Hi,     I need someone expert in PYMOL. I am getting a trouble to prepare a figure to display electron density for some water molecules. I can see clear density in COOT at sigma level 2.5. But, I could not see the density in PYMOL even at sigma level 1.0 Here is what I have done in PYMOL 1. file…….open ……..pdb and map files. I can see these two objects on the right column. 2. Then I selected the waters for which I want to display the electron density and created an object named ‘wat’ 3. In the command line I wrote ‘isomesh mesh1, 3fo2fc.map, 1.0, wat, carve=1.6’ and it creates an object ‘mesh1’ that shows the electron density of some of the waters (not all) selected in ‘wat’. I tried with other sigma levels, but the problem persists. I could not understand why for some waters electron density did not show up in PYMOL, but it does in COOT. I also noticed the same problem remains for part of this molecule, not just for some waters. I checked the pdb file, which looks fine and have the standard format. Does anyone have any idea, what’s going wrong? Thanks… Raja   Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!.