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,
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