[Chimera-users] Delphi electrostatic potential visualization

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 31 15:43:53 PDT 2014

Hi Joshua,
Thanks for your kind words!

I can't think of any reason why you couldn't have several different structures colored by several different maps.  My only idea in your first session is that perhaps the structure was rotated/translated separately from the map so that they were no longer correctly aligned with one another.  One must be careful not to change the spatial relationship between the structure and its corresponding map.

Maybe you were running DelPhi outside of Chimera because you couldn't get it to run via DelPhiController?  The link you sent is rather old advice and in more current versions of Chimera, the process may work.  However, if you find the separate process reasonably convenient, no reason to switch.

FYI, more recent versions of Chimera can also run APBS via web service (as well as PDB2PQR for prepping structures for APBS).

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 31, 2014, at 1:40 PM, Joshua Broyde <jb3401 at c2b2.columbia.edu> wrote:

> Hi,
> My name is Joshua Broyde, and I am a big fan of Chimera. I have recently been using Chimera to visualize Delphi outputs (i.e. .phi files).As per your advice here: http://plato.cgl.ucsf.edu/pipermail/chimera-users/2006-March/000710.html I have been using Delphi itself and visualizing the output in Chimera, rather than using the DelphiController within Chimera.
> Chimera seems to not consistently be able to visualize the output of Delphi on the surface of the proteins. After coloring 2 different protein models with the delphi electrostatic output, I tried to color the third protein surface I was examining with the Delphi output, and Chimera simply colored it gray. To double check that this was not a Delphi problem, I then took this protein structure and created a separate chimera session with it, and then Chimera was able to visualize the Delphi output on the protein surface. Is this a bug or something? Is there a way around this? I want to be able to visualize many Delphi outputs at once on Chimera.
> Thanks so much, you guys are great!
> Sincerely,
> Joshua Broyde 

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