Dear Chimera Users, I am interested in visualizing the electrostatic potential calculated by the APBS tool Chimera provides and I have several questions regarding this. 1) We have been having troubles running the PDB2PQR/APBS tools (I am not sure if we had trouble with both, it has been a few weeks) that Chimera provides, and I believe we fixed this by changing the version number at the very end of the web server address. Is there anything else we could have done to fix this? 2) I noticed that the numbers that are displayed when I visualize the APBS-calculated potential on the MSMS are very different from the numbers shown when I use the volume viewer (I mapped the values to atoms and then displayed those as labels). Why are those numbers not the same? Is it because the volume data will map the potential near the atoms and display that, whereas the potential on the surface (or actually 1.4 Angstroms from the surface) will display the potential value on the surface? Should I assume that the units are the same? 3) I am interested in finding the "patches" of the molecular surface the have fairly positive potential. I am familiar with the PatchFinderPlus server but I am interested in finding several patches, not just the largest one. I have not found any tool related to this in Chimera, please let me know if I am wrong. So,I found the redarea.py script avalaible from Chimera's website and I am thinking about modifying it in order to do this. The script iterates over all surface pieces. Is it possible to calculate the distance between vertices and atoms? Is it possible to obtain the potential value at a vortex? I think this would help me get started... Thank you very much, Christos Deligkaris, PhD Assistant Professor of Physics, Drury University 900 N Benton Ave, Springfield MO, 65802 Office Phone: (417) 873-7234 www2.drury.edu/christos <http://www2.drury.edu/christos/index.html> @DeligkarisGroup <https://twitter.com/DeligkarisGroup> +ChristosDeligkaris <http://google.com/+ChristosDeligkaris>