Electrostatic potential surface area
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
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 <yasser.almeida@gmail.com> 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
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@cgl.ucsf.edu> 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 <yasser.almeida@gmail.com> 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
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 <meng@cgl.ucsf.edu>:
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@cgl.ucsf.edu> 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 < yasser.almeida@gmail.com> 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
Hi Yasser, I added a feature request for a command to measure surface areas where a surface parameter like electrostatic potential is in a specified range. I think this makes more sense as a command than a mouse mode because you need to specify both the parameter of interest and the numeric range for that parameter. We’ll try to make such a command in our next generation ChimeraX program. Tom
On Apr 13, 2016, at 5:53 AM, Yasser Almeida Hernández wrote:
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 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 <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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participants (3)
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Elaine Meng -
Tom Goddard -
Yasser Almeida Hernández