[Chimera-users] Fwd: Coulombic Surface Coloring

[Francesco Pietra]

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


On Sun, May 3, 2009 at 10:50 PM, Eric Pettersen <pett at 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.html

  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
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>
>