Calculate surface area with with specified electrostatic potential

[Tom Goddard]

Yasser requests a magic wand mouse mode to compute surface areas where some surface parameter such as electrostatic potential is in a given range. Since the range needs to be specified, seems simpler to have a command do this.

Begin forwarded message:

From: Yasser Almeida Hernández
Subject: Re: [Chimera-users] Electrostatic potential surface area
Date: April 13, 2016 at 5:53:28 AM PDT
To: "chimera-users@… BB" <chimera-users@…>

Thanks for your reply! with a few modifications, I think I can do what I want.

On the other hand, it would be great that in futures developments of Chimera, create a mouse selection tool for surfaces patches, something like a "magic wound" like graphical packages like Photoshop or Gimp. In principle the idea would be select a surface according to a threshold value (ej. electrostatic potential) set by the user. With this, several selections could be created/added/subtracted, calculating the surface area and the ratio respect with the total area.

Regards

Yasser

2016-04-12 18:53 GMT+02:00 Elaine Meng :
Note that this script gets the area of the patches that are more red than blue, which is traditionally the part with negative potential. You could either subtract from the total area to get the positive-potential area, or do the coloring the opposite of the conventional way.

Elaine

On Apr 12, 2016, at 9:45 AM, Elaine Meng <meng@…> wrote:

Hi Yasser,
I believe Tom Goddard wrote a python script to do this a couple years ago… it is described in this previous post, with link for getting the script:

<​http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-December/009401.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

On Apr 12, 2016, at 1:25 AM, Yasser Almeida Hernández wrote:

Hi all,
I did some calculations of the electrostatic potential using APBS and Delphi. I want to calculate the surface area of a positive patch in my protein.
There is a way to select and compute the surface area/patch, filtering by the electrostatic surface value?
Thanks in advance
Yasser

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