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 ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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