[chimera-dev] Electrostatic coloring using Chimera

[Elaine Meng]

Hi Daniel,
I don't understand - what preselected electrostatic potential file are you talking about, and what tutorial says there should be such a thing?

There is a tutorial for coloring by Coulombic electrostatic potential, but it does not use any outside files, only the pdb 3eeb:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html>

At the end of the tutorial there is also a link to an electrostatic potential map from DelPhi, but that file is just in case people want to try coloring using a map in addition to the Coulombic coloring that was covered in the tutorial.

Also I hope you mean Chimera 1.7 (not 1.17)!

Maybe this recent post will clarify some things about electrostatic coloring in Chimera...
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-February/008472.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

p.s. chimera-dev is for programming questions - general questions should go to chimera-users at cgl.ucsf.edu and bug reports to chimera-bugs at cgl.ucsf.edu
<http://www.cgl.ucsf.edu/chimera/docs/feedback.html>

On Feb 15, 2013, at 1:32 PM, Daniel Lee wrote:

> To Chimera Developers,
> 
> Hello, this is Daniel Lee from University of Utah Department of Pharmaceutics and Pharmaceutical Chemistry. I am currently working as a Teaching Assistant in a DNA/Protein modeling class for graduate students. We are using UCSF chimera 1.17 to explore molecular structures. I have a hard time trying to get the system to show electrostatic surface with colors matching to the electronegativity. I followed the tutorials however it seems really difficult to reproduce what the tutorial did. Surface/binding analysis did not had the preselected electrostatic potential file. I looked through the system files however did not find anything. Would you be able to assist me with this issue?
> 
> The PDB model I was exploring was 2KTZ and 2KU0. I used the fetch function to download this file.
> 
> Thank you,
> Daniel
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