Dear all, I have posted this message also to the APBS list but have not yet had a response so if anyone here can help I'd be most grateful.
We are using APBS tools in Pymol to compare the electrostatic surfaces of two related proteins. We are concerned about the correct way to display these so that the comparison is meaningful. Our question relates to the effect of the overall charge of the protein and the contours at which the electrostatic potential is displayed. Specifically, the calculated net charge of one of the proteins is -18 and the other is -11 and if both are contoured between 4 and -4 one surface looks as though the charge density is exaggerated, i.e. there are very few patches without strong positive or negative charge. Should the net charge be considered when choosing how to contour the electrostatic surface? Cheers, Janet -- Dr Janet Deane Postdoctoral Researcher Sir William Dunn School of Pathology South Parks Rd University of Oxford OX1 3RE United Kingdom Phone: +44 1865 275385 Email: janet.de...@path.ox.ac.uk
