Hi James, Currently there is no Chimera command for electrostatic surface coloring. I am sure it could be done in python, but that is beyond my skill set. It is my understanding that the PCE server does not output the electrostatic potential map - I think it only provides the PQR file (simply the PDB file with extra columns with atomic radii and atomic partial charges, essentially the input to the ESP calculation rather than output), images from the DINO program of different orientations of the protein, and PDB with ESP values at the atom positions. I don't remember the format of the latter, but if the ESP values are in the B-factor column, you could use "Render by Attribute" in Chimera (under Tools... Depiction) to color by atom "bfactor" to show these values. However, I think it is much less useful to show the potential values at the underlying atoms rather than at the surface, especially if they are the same atoms used to calculate the potential in the first place. The only web server I have ever found that provides ESP map outputs is webPIPSA: Protein Interaction Property Similarity Analysis http://pipsa.eml.org It is focused on performing a calculation on multiple proteins and comparing them (won't let you proceed until you specify at least two), choice of using UHBD or APBS. webPIPSA input: upload PDB files or specify PDB IDs, email address for getting results webPIPSA output: dendrogram and heat map comparing the results for the multiple proteins, optional download of zip file with intermediate results (includes map files and corresponding PDBs) - my first attempt with two structures and align "none" and use UHBD failed...I guess you are only supposed to use "none" if the proteins are already superimposed, which they weren't because I didn't care about the comparison - second attempt with align option "sup2pdbs" and use UHBD was successful. In Chimera, should probably only view the maps along with the corresponding PDBs from the intermediate results since they may have been transformed (in the superposition step) I last tried it in May, resulting in the notes above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 22, 2008, at 9:16 AM, James Fethiere wrote:

Hi,

• is there a way to use the electrostatic surface coloring from the tools/surface menu, in a command file? It seems that it is only available through the menu? • I have a pqr electrostatic potential file calculated from the PCE server http://bioserv.rpbs.jussieu.fr/Help/PCE.html using MEAD. How do I get it into chimera?

Thanks