<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Edu,<br>
<br>
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.<br>
<br>
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<br>
<br>
chimera/share/MoleculeSurface/calcsurf.py<br>
<br>
This is also in the Chimera source code online<br>
<br>
<a class="moz-txt-link-freetext" href="http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/MoleculeSurface/calcsurf.py">http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/MoleculeSurface/calcsurf.py</a><br>
<br>
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.)<br>
<br>
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.<br>
<br>
chimera/bin/mscalc<br>
<br>
We'll be very interested to see your results and consider including
them in Chimera. Let us know if you run into problems.<br>
<br>
Tom<br>
<br>
<br>
<br>
-------- Original Message --------<br>
Subject: [chimera-dev] Fwd: SASA calculation in Chimera<br>
From: Elaine Meng <br>
Date: 11/15/11 9:06 AM<br>
<blockquote
cite="mid:0D8E370D-DD05-45A8-84F9-866086836CFA@cgl.ucsf.edu"
type="cite">Hi Edu,
<div>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.</div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>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.</div>
<div>Best,</div>
<div>Elaien</div>
<div>
<div>
<span class="Apple-style-span" style="border-collapse:
separate; color: rgb(0, 0, 0); font-family: Helvetica;
font-size: medium; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-align: auto; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-border-horizontal-spacing: 0px;
-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; ">
<div>-----</div>
<div>Elaine C. Meng, Ph.D. </div>
<div>UCSF Computer Graphics Lab (Chimera team) and Babbitt
Lab</div>
<div>Department of Pharmaceutical Chemistry</div>
<div>University of California, San Francisco</div>
<div><br>
</div>
</span></div>
<div>
<div>Begin forwarded message:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px;"><span
style="font-family:'Helvetica'; font-size:medium;
color:rgba(0, 0, 0, 1);"><b>From: </b></span><span
style="font-family:'Helvetica'; font-size:medium;">Eduardo
José Cepas Quiñonero<br>
</span></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px;"><span
style="font-family:'Helvetica'; font-size:medium;
color:rgba(0, 0, 0, 1);"><b>Date: </b></span><span
style="font-family:'Helvetica'; font-size:medium;">November
15, 2011 3:19:17 AM PST<br>
</span></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px;"><span
style="font-family:'Helvetica'; font-size:medium;
color:rgba(0, 0, 0, 1);"><b>To: </b></span><span
style="font-family:'Helvetica'; font-size:medium;">Elaine
Meng<br>
</span></div>
<div style="margin-top: 0px; margin-right: 0px;
margin-bottom: 0px; margin-left: 0px;"><span
style="font-family:'Helvetica'; font-size:medium;
color:rgba(0, 0, 0, 1);"><b>Subject: </b></span><span
style="font-family:'Helvetica'; font-size:medium;"><b>Re:
SASA calculation in Chimera</b><br>
</span></div>
<br>
Hi Elaine,
<div><br>
</div>
<div>I'm Edu, colleague of Horacio. I would like to ask you
several things related to the previous question he asked.</div>
<div><br>
</div>
<div>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).</div>
<div><br>
</div>
<div>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?¿</div>
<div><br>
</div>
<div>Then, after reading the link</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/sourcecode.html">http://www.cgl.ucsf.edu/chimera/sourcecode.html</a></div>
<div><br>
</div>
<div>we realize that this can be a really complex
purpose...:</div>
<div><br>
</div>
<div>"<span class="Apple-style-span" style="font-family:
'Times New Roman'; background-color: rgb(255, 255, 255);
font-size: medium; ">Compiling Chimera requires building
over 40 third-party packages and is not recommended</span>"</div>
<div><br>
</div>
<div>"<span class="Apple-style-span" style="font-family:
'Times New Roman'; background-color: rgb(255, 255, 255);
font-size: medium; "> </span><span
class="Apple-style-span" style="font-family: 'Times New
Roman'; background-color: rgb(255, 255, 255); font-size:
medium; ">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.</span>"</div>
<div><br>
</div>
<div><br>
</div>
<div>Could we have some help on this¿? Could you advice us?</div>
<div><br>
</div>
<div>Thanks in advance,</div>
<div>Edu.</div>
<div><br>
<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word">
<div>
<div><br>
<blockquote type="cite">
<div
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span
style="font-family:'Helvetica';font-size:medium"><b>From: </b></span><span
style="font-family:'Helvetica';font-size:medium">Elaine Meng<br>
</span></div>
<div
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span
style="font-family:'Helvetica';font-size:medium"><b>Subject: </b></span><span
style="font-family:'Helvetica';font-size:medium"><b>Re: SASA calculation
in Chimera</b><br>
</span></div>
<div
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span
style="font-family:'Helvetica';font-size:medium"><b>Date: </b></span><span
style="font-family:'Helvetica';font-size:medium">21 September , 2011
7:13:29 PM GMT+02:00<br>
</span></div>
<div
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span
style="font-family:'Helvetica';font-size:medium"><b>To: </b></span><span
style="font-family:'Helvetica';font-size:medium">Horacio Pérez-Sánchez<br>
</span></div>
<div
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span
style="font-family:'Helvetica';font-size:medium"><b>Cc: </b></span><span
style="font-family:'Helvetica';font-size:medium"><a
moz-do-not-send="true"
href="mailto:chimera-users@cgl.ucsf.edu"
target="_blank">chimera-users@cgl.ucsf.edu</a><br>
</span></div>
<div
style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><span
style="font-family:'Helvetica';font-size:medium"><b>Reply-To: </b></span><span
style="font-family:'Helvetica';font-size:medium">"<a
moz-do-not-send="true"
href="mailto:chimera-users@cgl.ucsf.edu"
target="_blank">chimera-users@cgl.ucsf.edu</a>
List" <<a moz-do-not-send="true"
href="mailto:chimera-users@cgl.ucsf.edu"
target="_blank">chimera-users@cgl.ucsf.edu</a>><br>
</span></div>
<br>
<div>Hi Horacio,<br>
Chimera is using MSMS to generate the
surface and give surface area values per
atom. There is more information and an MSMS
reference here:<br>
<br>
<<a moz-do-not-send="true"
href="http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces"
target="_blank">http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Computer Graphics Lab (Chimera team)
and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
On Sep 21, 2011, at 9:01 AM, Horacio
Pérez-Sánchez wrote:<br>
<br>
<blockquote type="cite">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:<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">a) where could we
find information about the SASA method
Chimera uses so we can test with our own
method<br>
</blockquote>
<blockquote type="cite">
b) same question for the method Chimera
uses to graphically render the molecular
surface<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Thanks in advance,<br>
</blockquote>
<blockquote type="cite">
Horacio<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<br>
</div>
</blockquote>
</div>
<br>
<div>
<span
style="border-collapse:separate;color:rgb(0,
0,
0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><span
style="border-collapse:separate;color:rgb(0,
0,
0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium">
<div style="word-wrap:break-word">
===============================================================================================<br>
Horacio Pérez-Sánchez, PhD<br>
Grupo de Arquitectura y Computación
Paralela<span> </span><span
style="white-space:pre-wrap"> </span>
| Parallel Computer
Architecture Group<br>
Departamento de Ingeniería y Tecnología de
Computadores | Computer Engineering
and Technology Department<br>
Facultad de Informática<span> </span><span
style="white-space:pre-wrap"> </span>| School
of Computer Science<br>
Universidad de Murcia<span
style="white-space:pre-wrap"> </span>|
University of Murcia<br>
Campus de Espinardo - 30080 Murcia (Spain)<br>
===============================================================================================<br>
<br>
<br>
<br>
<br>
<br>
<br>
</div>
</span></span>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
</body>
</html>