[Chimera-users] ESP grid is offset from original PDB coordinates??

Elaine Meng meng at cgl.ucsf.edu
Tue May 29 10:15:47 PDT 2007

On May 29, 2007, at 8:52 AM, Kenward Vaughan wrote:
> I was playing with esp results yesterday from Delphi on several
> structures, and ran a quick calculation on 2ace.  To my surprise, the
> results as visualized as a solid under volume viewer were very  
> obviously
> offset from the structure itself.  They stand alone to one side of the
> original.  I've attached a small jpg of this.

Hi Kenward,
I tried calculating ESP for 2ace with DelPhiController in 1.2415 on a  
couple of platforms (albeit neither linux) but could not reproduce  
the problem.  In this version of Chimera, Volume Viewer does not  
automatically appear when the ESP is calculated, but if I do open  
Volume Viewer and display surface or solid, the "blobs" are all on in  
the same place as the protein.  I attached an example of the  
"surface" display in Volume Viewer at the default contour level (the  
"solid" display also overlaps the protein, but the spots are fainter  
at the default contour level).  I just used the default radius and  
charge files and run parameters in delphi.

Here are some things to check:
- were the models separately transformed?  Maybe if you use the  
"reset" command, they will come back into register.

- is the grid box surrounding the protein or is it totally offset?   
Show a box outline in Volume Viewer (Features... Data display  
options, check the "Show outline box" option) to check this.

- are you using DelPhiController?  if so, the grid should  
automatically center on the molecule.  If you are running delphi in  
standalone fashion, however, there are some parameters exposed that  
could give you an offset that is not centered on the protein - make  
sure you aren't specifying such offsets in the delphi input file.

Other than that, I'm stumped...
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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