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

Kenward Vaughan kvaughan at bc.cc.ca.us
Wed May 30 00:03:52 PDT 2007

On Tue, 2007-05-29 at 10:15 -0700, Elaine Meng wrote:
> 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

Hmm.  Did I mention IANADPE (I Am Not A Delphi Expert.)?  

I turned around and tried to duplicate it, with no success.  Since I
know I didn't hallucinate the event, I backtracked a bit.  Changing the
settings in DelphiController didn't seem to help.  

I then went further back into my memory of that particular run, and
realized where the issue lay.  I had done the same on another structure,
then closed the session, then opened 2ace.pdb.  Repeating this sequence
recreated the problem.

I have not exhaustively tried various examples, but for at least a
subset of files, the following replicates the problem:

1) open a pdb and run Delphi, followed by Volume Viewer to see the

2) close the session (but not Chimera),

3)  repeat #1 on another pdb file.

I don't know if it has to do with not clearing out the old default.phi
file or perhaps some other internal variable, but at least I'm at ease
now... ;-)

BTW, I've found that selecting a chain the first time after opening a
pdb file causes the backgound to turn green (with envy?).  This clears
after a second chain selection...


Dr. Kenward Vaughan                    `:,'~~~~~
Professor of Chemistry                 \;:/
Bakersfield College                    |,;|
1801 Panorama Drive                   / ', \
Bakersfield, CA  93305               / o  O \
http://www2.bc.cc.ca.us/kvaughan    (oOoOOoOo)

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