<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Sean,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I find that these structures surface on my Mac, but do fail on the Windows machine I tried. There is a workaround I recently found that isn't mentioned in the messages Elaine listed and that is to split the model into separate models on a per-chain basis and then surface those models. This works for both the structures your mentioned, but of course might be awkward to work with depending on what you intend to do after surfacing. Anyway, to do the splitting/surfacing open the command line (Favorites->Command Line) and type:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>split</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>surf</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>We intend to replace our current surfacing library (MSMS) with our own custom library in our next release, but that won't be until the middle of this year.</div><div><br></div><div>--Eric<br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Mar 5, 2009, at 4:34 PM, Elaine Meng wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Sean,<br>Unfortunately it is a very common problem relating to numerical <br>failure of the MSMS code on certain structures, and is listed in our <br>known bugs. We have been working on our own code to replace MSMS, but <br>it is not available yet. There are many possible things to try to <br>avoid the problem, but it is very trial-and-error and different for <br>each structure.<br><br>It is helpful when reporting a problem to say what version of Chimera <br>you are using, since there have been some improvements throughout time <br>(although not eliminating the problem completely). It might help to <br>get a newer version of Chimera, or it might not.<br><br>Please see these previous posts for more information and workaround <br>suggestions:<br><br><<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html</a> <br><blockquote type="cite"><br></blockquote><<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html</a>><br><<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/">http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/</a> <br>002954.html><br><br>I hope this helps,<br>Elaine<br>-----<br>Elaine C. Meng, Ph.D. <a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a><br>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>Department of Pharmaceutical Chemistry<br>University of California, San Francisco<br> <a href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</a><br><br><br><br>On Mar 5, 2009, at 2:08 PM, Du, Sean wrote:<br><br><blockquote type="cite">Dear Chimera developers and sophisticated users,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have trouble to show the surfaces of serveral crystal structures, <br></blockquote><blockquote type="cite">including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I <br></blockquote><blockquote type="cite">would get pop-up error window and the following message in my Reply <br></blockquote><blockquote type="cite">Log:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0<br></blockquote><blockquote type="cite">Surface calculation failed, mscalc returned code 5<br></blockquote><blockquote type="cite">C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0<br></blockquote><blockquote type="cite">Surface calculation failed, mscalc returned code 5<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Since I don't have problem with other pdb files, such as 3dnn, I <br></blockquote><blockquote type="cite">wonder if this problem is simply associated with some particular pdb <br></blockquote><blockquote type="cite">files? If anyone out there knows a few tricks to overcome this, I'd <br></blockquote><blockquote type="cite">really appreciate it.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Many thanks in advance,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Sean<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>