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

Elaine Meng meng at cgl.ucsf.edu
Wed May 30 09:56:19 PDT 2007

Hi Kenward,
Aha!  It turns out that when you use "Close session," the Input  
"Molecule" in DelPhiController is not automatically cleared.  When  
you open subsequent structures, you have to go to the Input section  
of DelPhiController and click "Browse" again to use a structure that  
is actually open.  Otherwise, it will keep calculating the ESP for  
your original model even though it was closed already (I guess the  
information has been stored somewhere).  If you didn't reset the  
Input, you are probably seeing the ESP for the first structure on  
which you used DelPhiController since Chimera was started, even  
though it's a new map with the new name indicated in the Output section.

I would classify this as a Chimera bug, or at least bad behavior,  
rather than user error!  Thanks for reporting this,
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

On May 30, 2007, at 12:03 AM, Kenward Vaughan wrote:

> 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
> results,
> 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...
> HTH,
> Kenward

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