Hi Bala, In version 1.4 (you would need to get a recent daily build, not the production release) there is a Coulombic Surface Coloring tool under Tools... Surface/Binding Analysis. The documentation describes how it works: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic...
It will assign charges to your structure. It doesn't matter where the PDB file is from, except that it should be in correct PDB format and have standard atom names for standard residues so that they can be recognized correctly by the charge assignment step. Sometimes there are some format problems with PDB files created by Amber, however, so be sure to check in the Reply Log to see if there were problems with charge assignment. If there are, you may need to manually edit the file to correct any format problems. There is also an "Electrostatic Surface Coloring" tool, but it requires an electrostatic potential map previously calculated with some other program such as DelPhi, APBS, or UHBD. 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 Apr 15, 2009, at 9:10 AM, Bala subramanian wrote:
Friends, How to do electrostatic coloring based on partial charges. I have a pdb generated from amber, i would like to assign amber charges and color the surface using assigned charges. Bala