[Chimera-users] Coulombic Surface Coloring

Eric Pettersen pett at cgl.ucsf.edu
Sun May 3 13:50:29 PDT 2009

Hi Francesco,
	How did you find the page describing Coulombic Surface Coloring, did  
you Google it?  Anyway, that tool is only in the daily build, and not  
in whatever version you are using.  You can get a daily build by going  
to the Chimera home page (www.cgl.ucsf.edu/chimera) and following the  
"Daily Builds" link.  You can install in a location different from  
your current version if you like.  That way you can use the daily  
build for the surface coloring, but use the other version if needed  
(i.e. if you run into a bug).
	If your protein consists only of standard residues then I see no  
reason for you to use your calculated charges -- the pre-computed  
Amber charges should be fine.  If there are non-standard residues then  
it's up to you if you want to use Define Attribute to add the charges  
to the structure or instead rely on Chimera's charge-computation  


	Eric Pettersen
	UCSF Computer Graphics Lab

On May 3, 2009, at 12:07 PM, Francesco Pietra wrote:

> Hi:
> I would like to simply color the surface of a protein by the Coulombic
> Surface Coloring method. I can show the surface, have a file with
> calculated charges if useful, but i am unable to implement the
> indications below
> "There are several ways to start Coulombic Surface Coloring, a tool in
> the Surface/Binding Analysis category.
> The molecular surface(s) should first be displayed (using Actions...
> Surface... show or the command surface) and then chosen from the list
> of Surfaces to color by ESP. "
> which tool should be opened from Surface/Binding Analysis? Of those
> related, I can only see Electrostatic Surface Coloring and that - in
> my hands - does not bring to the simple Coulombic method.
> Thanks for clearing
> francesco pietra
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