Hi Raja,
If you are reading in the map saved from coot, it covers just the AU. Most likely the selection that you are trying to show the mesh around in pymol is outside of the AU. The solution is to use FFT to draw maps around your model (it an option in one of the drop down menus in the FFT CCP4i gui) and use these maps in pymol. And don't forget to add the .ccp4 extension to the map files for reading into pymol.
hope that solves your problem.
Eric
__________________________
Eric Larson, PhD
MSGPP Consortium
Department of Biochemistry
Box 357742
University of Washington
Seattle, WA 98195
On Thu, 11 Feb 2010, 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
>
>
>
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