Hi Edu, Chimera uses MSMS to calculate solvent excluded surfaces (SES) and per-atom values of solvent excluded surface area (SESA) and solvent accessible surface area (SASA). Chimera does not currently display solvent accessible surfaces, only solvent excluded surfaces. To do these calculations Chimera calls a standalone program that I wrote called mscalc which uses the MSMS library. The mscalc program takes two command-line arguments: probe radius and vertex density. Then it reads from standard input an integer N saying how many atoms there are followed by an N by 4 array of (x,y,z,radius) float values describing the centers and radii of each atom. It writes the results to standard output including triangles composing the surface and areas per-atom. Both the input xyzr array and the output are in binary (not text) format. Calling the standalone program is done by Python code in your Chimera distribution chimera/share/MoleculeSurface/calcsurf.py This is also in the Chimera source code online http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/MoleculeSurface/ca... Take a look at the run_mscalc and parse_mscalc_output functions to see exactly how the output of the mscalc program is formatted. The mscalc C program is attached to this email. (It is not online because we keep it with the MSMS source code which we are not allowed to release because of licensing issues.) You should be able to simply replace the Chimera mscalc program in your copy of Chimera with your own program that takes equivalent input and produces equivalent output. chimera/bin/mscalc We'll be very interested to see your results and consider including them in Chimera. Let us know if you run into problems. Tom -------- Original Message -------- Subject: [chimera-dev] Fwd: SASA calculation in Chimera From: Elaine Meng Date: 11/15/11 9:06 AM
Hi Edu, I don't do any of the Chimera programming (I do testing, documentation, web content), so I can only forward your question to the developers/programmers.
It may be possible to have your surface calculation as a separate extension instead of integrated into the Chimera core, but I'm guessing integration has some advantages... perhaps computational efficiency?
Programmers who have worked on surface calculations in Chimera should have better or more complete answers for you. However, please bear with us, as this week is especially busy for our group. Best, Elaien ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Begin forwarded message:
*From: *Eduardo José Cepas Quiñonero *Date: *November 15, 2011 3:19:17 AM PST *To: *Elaine Meng *Subject: **Re: SASA calculation in Chimera*
Hi Elaine,
I'm Edu, colleague of Horacio. I would like to ask you several things related to the previous question he asked.
As Horacio said before, we have developed a new SASA calculation method. Our intention is to integrate it into Chimera, as another way to calculate the data Chimera needs to show molecular solid surfaces (instead of using msms).
Since Chimera doesn't call msms executable, but it has msms integrated into it, we assume that whe have to adapt our method to Chimera, and compile both together, right?¿ If not, Is there another simple way to change the method Chimera uses to calculate molecular surfaces?¿
Then, after reading the link
http://www.cgl.ucsf.edu/chimera/sourcecode.html
we realize that this can be a really complex purpose...:
"Compiling Chimera requires building over 40 third-party packages and is not recommended"
"creating a full build-from-source copy of Chimera is a lot of work and depends on getting a bunch of things in the build environment set up just right for your particular platform. Currently we do not have any documentation describing the build environment or procedure."
Could we have some help on this¿? Could you advice us?
Thanks in advance, Edu.
*From: *Elaine Meng *Subject: **Re: SASA calculation in Chimera* *Date: *21 September , 2011 7:13:29 PM GMT+02:00 *To: *Horacio Pérez-Sánchez *Cc: *chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> *Reply-To: *"chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> List" <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>
Hi Horacio, Chimera is using MSMS to generate the surface and give surface area values per atom. There is more information and an MSMS reference here:
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfac...>
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 Sep 21, 2011, at 9:01 AM, Horacio Pérez-Sánchez wrote:
We have developed a fast and accurate new GPU based SASA calculation method. It can bring information about SASA per atom and also grid per atom necessary to graphically render the molecular surface. We are new to Chimera but we would like to know:
a) where could we find information about the SASA method Chimera uses so we can test with our own method b) same question for the method Chimera uses to graphically render the molecular surface
Thanks in advance, Horacio
=============================================================================================== Horacio Pérez-Sánchez, PhD Grupo de Arquitectura y Computación Paralela | Parallel Computer Architecture Group Departamento de Ingeniería y Tecnología de Computadores | Computer Engineering and Technology Department Facultad de Informática| School of Computer Science Universidad de Murcia| University of Murcia Campus de Espinardo - 30080 Murcia (Spain) ===============================================================================================