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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