<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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 <<a href="mailto:ecepasqui@gmail.com">ecepasqui@gmail.com</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; 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 <<a href="mailto:meng@cgl.ucsf.edu">meng@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; 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 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 <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@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>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 <<a href="mailto:horacio@um.es" target="_blank">horacio@um.es</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>Cc: </b></span><span style="font-family:'Helvetica';font-size:medium"><a 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 href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a> List" <<a 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 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>Email: <a href="mailto:horacio@um.es" target="_blank">horacio@um.es</a><br>Tel: <a href="tel:%2B%2034%20868%2088%208509" value="+34868888509" target="_blank">+ 34 868 88 8509</a><br>
===============================================================================================<br><br><br><br><br><br><br></div></span></span>
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