Hi Kevin, If you click the Help button on the Coulombic Surface Coloring tool, it will bring up the man page with all the details in the browser window. The documentation is included with your download, but here are the corresponding pages on our Web site: Coulombic Surface Coloring: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic...
... "The calculation requires charge assignments, which in turn require hydrogens. An existing structure lacking hydrogens is not changed, but a copy is created in memory, protonated, and assigned charges, which are then transferred to the existing structure. Where hydrogens are missing from the existing structure, their charges are collapsed onto the adjacent heavy atom." ... Details of charge assignment: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge...
You will need to decide what level of detail is appropriate for your legend. It could be as little as something like "colored by Coulombic electrostatic potential in Chimera" if you've also included a color key, or include more technical details such as the name of the tool, Chimera version, dielectric value, your choice of histidine protonation states, what colors correspond to what values etc. as one would need to reproduce the figure. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Dec 11, 2009, at 12:39 PM, Kevin Dalby wrote:
Dear Elaine I am planning to generate a couple of figures using the new coulombic surface coloring tool. Can you give me any pertinent details that I might include in the Figure legend describing how the surface is generated. thanks Kevin Dalby