---------- Forwarded message ---------- From: Francesco Pietra <chiendarret@gmail.com> Date: Sun, May 3, 2009 at 11:01 PM Subject: Re: [Chimera-users] Coulombic Surface Coloring To: Eric Pettersen <pett@cgl.ucsf.edu> On Sun, May 3, 2009 at 10:50 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Francesco,        How did you find the page describing Coulombic Surface Coloring, did you Google it?

Yes, http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/coulombic/coulombic...   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).

I'll first see if a program to furnish data for Chimera's Electrostatic Surface Coloring is available. Any suggestion? I forgot that have both apbs and delphi executables as components of an installed docking program.

       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 capabilities.

My "have a file with calculated charges" was misleading, It was a mol2 file saved with Chimera. thanks francesco

--Eric

       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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users