Hi Ricardo –
This question is probably best addressed to the PyMOL mailing list.
The rate of change in the potential value (the speed of change in the colors) is related to the local field density and the local heterogeneity in charge distribution.
If you see parts of the protein left out of the calculation, then you should increase the grid lengths in the APBS/PyMOL dialog and perhaps re-examine the grid center settings.
Hope this helps!
Pacific Northwest National Laboratory
From: Ricardo O. S. Soares [mailto:email@example.com]
Sent: Thursday, May 05, 2011 1:23 PM
Subject: [Pdb2pqr-users] APBS visualization issues
I'm having some trouble with APBS 2.1 visualization, if anyone can help me I'd be grateful.
There are positions in the protein where the blue converges slowly to white and then to red, and other which there are no gradation between blue and red. Why is that?
Also, sometimes within pymol the grid leaves a part of the protein out of the calculation, has anyone already seen it?
Thanks in advance!