<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="">Hi Sarah,<div class=""><br class=""></div><div class=""> It is frustrating that the Chimera solvent excluded surface code is not reliable. We replaced that code in our next generation ChimeraX program which is not yet released. But the new surface calculation is also in Chimera if you use a secret grid option, command</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>surface #3 grid 0.5</div><div class=""><br class=""></div><div class="">The value is the grid spacing, 0.5 Angstroms works well. This calculation will always work, but we don’t advertise this because the resulting surface does not know which atoms are associated with which surface patches. (We just put it in Chimera for some basic testing.) But you can use this surface for electrostatic coloring.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Nov 9, 2016, at 3:50 PM, Sarah Piper <<a href="mailto:s.piper@imb.uq.edu.au" class="">s.piper@imb.uq.edu.au</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi everyone,
<div class=""><br class="">
</div>
<div class="">I’ve been struggling with getting the structure surface of my molecule shown (actions surface - show). Even after going through a list of suggestions of how to overcome this problem (e.g.
<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html" class="">
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html</a> ), I can’t get all needed surfaces displayed.</div>
<div class=""><br class="">
</div>
<div class="">Some other .pdb files work without a problem, but mine doesn’t or just works partially (e.g. just one chain instead of all chains), without seeing any apparent differences in the .pdb files or molecule sizes.</div>
<div class=""><br class="">
</div>
<div class="">A while ago I did not encounter this problem (using the same molecule/file), so is this maybe a chimera version problem? </div>
<div class="">Or do the .pdb files have to be in a certain format?</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I usually get the following errors:</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">"Surface calculation failed, mscalc returned code 2.</div>
<div class=""><br class="">
</div>
<div class="">Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure
is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at</div>
<div class=""><br class="">
</div>
<div class=""><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html" class="">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html</a>”</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">My main use of surfaces in chimera is to display electrostatic potential files (or hydrophobicity plots) calculated in APBS and others. I’m using Chimera v1.9 on a Mac (but I had the same problems on a Linux workstation).</div>
<div class=""><br class="">
</div>
<div class="">I'd appreciate any feedback or reply!</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Many thanks for your help,</div>
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Sarah</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<br class="">
<br class="">
<div apple-content-edited="true" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
…………………………………………………………………..</div>
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Sarah Piper, PhD student</div>
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
University of Queensland, St Lucia, 4072 QLD, Australia</div>
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
<br class="">
</div>
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Phone: +61 7 3346 2325<br class="">
Email: <a href="mailto:sarah.piper@uq.edu.au" class="">sarah.piper@uq.edu.au</a><br class="">
<br class="">
<br class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</div>
_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>