On Wed, Feb 10, 2010 at 12:16 PM, Raja Dey <[email protected]> wrote:
> 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? > What format is the map? If it's in XPLOR format, this is probably the source of the problem - it lacks symmetry information and only covers a pre-determined portion of the unit cell. Try leaving out everything after the sigma level when you run the 'isomesh' command, and you'll get some idea of the coverage. PS. There is a PyMOL mailing list too: https://lists.sourceforge.net/lists/listinfo/pymol-users -Nat
