[Chimera-users] Coloring by Delphi potential in Chimera
meng at cgl.ucsf.edu
Fri Jul 29 14:53:58 PDT 2005
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
(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
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
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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