[Chimera-users] ESP grid is offset from original PDB coordinates??
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...
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
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 \
More information about the Chimera-users