VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 10 2004 - 11:19:55 CST

Hi,
  The automatic normalization you asked about is controlled by the
color scale settings in the 'trajectory' tab of the graphical
representations window. If you set the "color scale data range"
manually, VMD will not use the normalized values and will instead use the
values you select as the min/max values between which a color ramp is
generated. Let us know if you need more help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 10, 2004 at 02:10:27PM +0100, Florian Barth wrote:
> Hello,
>
> I have done some protein-ligand dockings and I'm using vmd 1.8.2/linux
> to visualize the docked ligand conformations (trajectory pdb format). I
> would like to color the conformers by docking energy and therefore I
> have inserted the energy value for each into the occupancy field of the
> pdb file. Of course, the energy is the same for every atom of one
> confomer, there are only changes between different conformations. But it
> appears that vmd normalizes the values for each molecule, because all
> molecules have the same color when using the occupancy coloring method.
> Is there any way have the molecules colored according to predefined
> (floating-point-)values in the pdb file?
>
> Thanks,
>
>
> Florian Barth 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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