From: John Stone (
Date: Mon Feb 05 2007 - 11:03:04 CST

  I've loaded your CHARMM PBEQ data successfully and viewed it
as an Isosurface with volume coloring. The VMD saved state you
included in the directory on BioCoRE was not set to color the
surface by "Volume", so you wouldn't have seen any colors regardless
what video card/system you used if you were using those settings.
Secondly, after enabling volumetric coloring in VMD, I noticed
that your potential map value range is quite small. I didn't see
much in the way of potential colors until I made the color scale
data range very small, with a min of 0.2 and a max of 0.2. This
range of values seems unusually small to me, but I don't know what
units CHARMM's PBEQ module is exporting, so it might be the expected
range of results for your molecule. In any case, I've attached a new
VMD saved state to this email which sets the various viewing
parameters so you can see the potential coloring. I edited the filename
in the saved state so it was a relative path (rather than /hom/Ivana/...)
so you'll need to "cd" to the directory where your PBEQ map is before
loading this saved state, or otherwise edit the "mol new" command
for the correct location of your dataset before running it in VMD.

  John Stone

On Mon, Feb 05, 2007 at 10:46:47AM -0500, ivana adamovic wrote:
> I am not sure if you got this e-mail, which I sent couple of days ago,
> so just in case I am resending it...
> Thanks a lot for your time and help,
> Ivana
> ======================
> Dear John,
> I have tried to load my CHARMM potential file by choosing FILE> new
> molecule> Determine the file type> CHARMM PBEQ Binary Potential Map
> Then I made sure that Drawing method is Isosurface and that:
> Draw is: Solid Surface
> Show: Box +Isosurface
> Now I get box and white doted molecule (changing Isovalue I can get
> almost white surface, or in the opposite direction just dots);
> Then I set Trajectory> color Scale Data range to -8.00 to 8.00 (it was
> 0 0), but it is still white ...
> I have left (on Biocore website VMD (Public) in the folder charmm.pbeq):
> 1. vmd.charmm.pbeq (saved state, so that you can see my final result) and
> also
> 2. jws.s1.phi.0.6.pbeq (CHARMM el. potential)
> Could you please check it out?
> Is this an issue with right plugin (I am not sure if I have that
> update you are mentioning, I just have pbeqplugin that you gave with
> charmm example) or is it something else ?
> Thanks a lot for your time and help!
> Ivana

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