[Chimera-users] Colouring castp surfaces by apbs electrostatic potential - how reliable is it?

Boaz Shaanan bshaanan at exchange.bgu.ac.il
Mon Mar 11 15:51:47 PDT 2013

Thanks a lot Elaine. That's good to know.


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710

From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Tuesday, March 12, 2013 12:41 AM
To: בעז שאנן
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Colouring castp surfaces by apbs electrostatic potential - how reliable is it?

Hi Boaz,
Sounds perfectly reasonable to me -- that CASTp surface is actually just parts of the molecular surface calculated by Chimera (using MSMS).  Although the area/volume values in the pocket list dialog are those calculated by castp, the display is the Chimera molecular surface for just the set of atoms reported by castp to comprise the pocket, minus any disconnected bits.

After displaying the surface for any pocket, you can see the MSMS surface model for the protein listed in the Model Panel, for example.

Thus you can feel free to use any of the surface-coloring approaches in Chimera that you like (APBS ESP, Coulombic ESP, residue conservation, etc. etc.), and just uncheck "colored by hydrophobicity" in the CASTp pocket list dialog.  That option was just provided for convenience because people often like to evaluate pocket hydrophobicity.

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

On Mar 11, 2013, at 3:14 PM, Boaz Shaanan wrote:

> Hi,
> I'd like to colour a surface generated by castp by electrostatic potential rather than by the hydrophobicity  values. I read in the .dx file from apbs and colour accordingly. The result makes sense to me in terms of +ve/-ve values,as obtained by "walking" on the surface (using the mouse) and taking into account the low dielectric values that apbs assigns to residues inside the protein during the calculation. Am I missing something about the way chimera handles the .dx file and doing something completely insane?
> Thanks for your input.
>                  Boaz

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