[Chimera-users] Coulombic surface coloring

[Elaine Meng]

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.html 
 >
...
"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.html#standard 
 >

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