[Chimera-users] Delphi electrostatic potential visualization

Tom Goddard goddard at sonic.net
Thu Jul 31 15:38:31 PDT 2014


Hi Joshua,

  There is no limit to how many surfaces Chimera can color using electrostatic potential.  The trouble is probably that your Delphi map is not covering the molecular surface, in fact your surface probably lies entirely outside the box containing the Delphi map and in this case the Surface Color dialog colors the surface gray.  You can check this theory using the Options button on the Surface Color dialog and changing the “Color outside volume” color, then press “Color” and see if your surface becomes that new color.  To see where the Delphi map is located relative to your protein you can display an outline around it, for example if the map is model #5 then use "vol #5 showoutline true”.

	Tom


On Jul 31, 2014, at 1:40 PM, Joshua Broyde 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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