[Chimera-users] Coloring by Delphi potential in Chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 29 14:53:58 PDT 2005

Hi Zach,
DelPhiViewer got removed because other tools can do the same things in 
a more general and flexible way.  Unfortunately in the latest snapshot 
(1.2129, June) it is confusing to get to these newer features, but they 
are all there, and I'll explain how.  I'll assume you are using that 
latest snapshot and that you have an electrostatic potential file in 
the format from DelPhi.
First, open the electrostatic potential file with File... Open.  If the 
file is named  ending in .phi  you can set the File type to "all (guess 
type)" or "DelPhi or GRASP potential".  This will automatically start 
Volume Viewer.

(A)  IF you want to look at contour (isopotential surfaces), keep using 
Volume Viewer.  Open the Volume Viewer man page by clicking the Help 
button on the dialog.  You probably want to go to the "Surface or Mesh" 
section of the man page, under "Display Panel".  Otherwise...

(B)   IF you want to color the molecular surface or GRASP surface based 
on the potential,
click the Unshow button on Volume Viewer and then the Close button on 
Volume Viewer.

Open the molecule and show its surface that you want to color, or open 
the GRASP surface you want to color (this can also be opened with 
File... Open).

The tool for coloring a surface by potential is Surface Color (Tools... 
Analysis... Surface Color).  Pick the surface of interest from the menu 
next to "Color surface" and choose the electrostatic potential data 
from the menu next to "Using volume data or geometry".  You probably 
want to change the "Color scheme" to "3 color symmetric" - then you 
have something similar to the DelPhiViewer surface coloring interface.  
Click the Help button on the Surface Color dialog if you want to see 
the man page.
We realized this is pretty confusing and have tried to make it better 
(and the improvements will show up in the next release).  The 
improvements are that you  will be able to color a surface according to 
electrostatic potential  by choosing Tools... Surface/Binding 
Analysis... Electrostatic Surface Coloring, and then you can open the 
electrostatic potential using a Browse button on that tool (avoiding 
Volume Viewer entirely).  It will also start with the 3-color scheme 
when opened this way.

I hope this helps,
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

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