<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi Hsin-Yi,</div><div class=""><br class=""></div><div class=""> There are lots of messages on the Chimera mailing list about how to identify surface exposed residues, for example,</div><div class=""><br class=""></div><a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006336.html" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>http://plato.cgl.ucsf.edu/pipermail/chimera-users/2011-May/006336.html</a><div class=""><br class=""></div><div class="">You can search the mailing list from the Chimera documentation web page:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/docindex.html" class="">http://www.cgl.ucsf.edu/chimera/docindex.html</a></div><div class=""><br class=""></div><div class="">The multiscale tool makes surfaces for each chain. To make surfaces of any set of selected atoms use the molmap command, for example, “molmap sel 5” to make a 5 Angstrom resolution surface. Here are molmap docs:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html" class="">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</a></div><div class=""><br class=""></div><div class="">Those surfaces can be exported as OBJ with menu File / Export Scene….</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 23, 2015, at 11:09 AM, Hsin-Yi Yeh <<a href="mailto:hyeh@cse.tamu.edu" class="">hyeh@cse.tamu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi,<div class=""><br class=""></div><div class="">I try to render a protein molecule to a geometry format (from .pdb format to .obj format) by Chimera. I use 'Multiscale models' tool in 'Higher-Order Structure' choice and then make the model by resurfacing at some appropriate resolution. It turns out that the whole protein molecule can be modeled pretty nicely. </div><div class=""><br class=""></div><div class="">However, I now have a similar problem; instead of rendering the whole protein molecule, I would like to render the whole structure separately. I want to render the exposed residues (those residues on the surface) and non-exposed/buried residues separately, so I will have two obj files (one for the exposed residues and the others for the non-exposed residues).</div><div class=""><br class=""></div><div class="">I haven't been able to figure this problem out yet. Thus, I am wondering could you please give me some direction? Any advice will be greatly appreciated!</div><div class=""><br class=""></div><div class="">Thank you,</div><div class=""><br class=""></div><div class="">Hsin-Yi (Cindy) Yeh<br class=""></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><span style="font-size:12.8000001907349px" class="">Hsin-Yi (Cindy) Yeh</span><div style="font-size:12.8000001907349px" class="">PhD Student</div><div style="font-size:12.8000001907349px" class="">Parasol Lab, <span style="font-size:12.8000001907349px" class="">Department of Computer Science and Engineering</span></div><div style="font-size:12.8000001907349px" class="">Texas A&M University</div><div style="font-size:12.8000001907349px" class="">Email: <a href="mailto:hyeh@cse.tamu.edu" target="_blank" class="">hyeh@cse.tamu.edu</a></div><div style="font-size:12.8000001907349px" class=""><a href="https://parasol.tamu.edu/people/hyeh/" target="_blank" class="">https://parasol.tamu.edu/people/hyeh/</a></div></div></div></div>
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