Thanks, Tyler. One thing I don’t understand about what you wrote: when you pick a color on an already-displayed contour, which color (of the usual 3 colors in the ramp) gets set? And how does this affect the colors in a slice instead?


I updated the Pymol Wiki with what I figured out (with help from Keith Callenberg). See: Detailed instructions on one way to do what I wanted (there may be a better way!) It’s Example #2 (with an illustrative image).


Thanks for your help,



From: Harmon, Tyler S []
Sent: Wednesday, 16 March 2011 14:17
To: Borhani, David; ''
Subject: RE: Change slice contour levels in APBS/pymol?


If you are using the plug in menu then after you have run apbs, it shows the visualization menu where the bottom middle and bottom right boxes are the isosurfaces options.  There is an adjustable box for each that changes the potential of the contour.  After it is already displaying the contour you can click on the color menu on the main display and choose any color that you want.


Let me know if that doesn’t help,



From: Borhani, David []
Sent: Tuesday, March 15, 2011 12:42 PM
To: ''
Subject: [Apbs-users] Change slice contour levels in APBS/pymol?


Is there a way to change the default slice contours of 1 kT/e shown by ABPS plugin in pymol, as you can for the isosrufaces and the molecular surface? Also, how does one change the colors?





David Borhani, Ph.D.

D. E. Shaw Research

120 West Forty-Fifth Street, 39th Floor

New York, NY 10036