<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">If you <i>do</i> decide to try to implement it yourself, you could write it as a Chimera Python script that creates "pseudobonds" for the struts you need. You would get a pseudobond group for the struts with this call:<div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>from chimera.misc import getPseudoBondGroup</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>pbg = getPseudoBondGroup("struts")</div><div><br></div><div>You would then add a pseudobond between atoms a1 and a2 with:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>pbg.newPseudoBond(a1, a2)</div><div><br></div><div>The pseudobonds would be treated the same as all other pseudobonds (e.g. hydrogen bonds, distance monitors) and would appear in Chimera's X3D/STL/VRML output.</div><div><br></div><div>You could ask further scripting questions on this list.</div><div><br></div><div>--Eric<br><div><br><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></div></span></div><div>On Apr 19, 2011, at 2:53 PM, Greg Couch wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <div text="#000000" bgcolor="#ffffff"> So yes, we are willing to incorporate a strut algorithm into UCSF Chimera, but right now, that code would need to be written by someone else. I suspect that George Phillip's original Python code would be a better starting point than the Jmol Java code. Another good starting point would be the pioneering work done by MSOE that is given in their RasMol Training Guide, Section III, "Designing a Model to be Built on the Rapid Prototyping Machines", <a href="http://www.rpc.msoe.edu/cbm/resources/rasmol.php">http://www.rpc.msoe.edu/cbm/resources/rasmol.php</a>.<br> <br> -- Greg<br> <br> On 04/17/2011 01:18 PM, <a class="moz-txt-link-abbreviated" href="mailto:moneal@notes.cc.sunysb.edu">moneal@notes.cc.sunysb.edu</a> wrote: <blockquote cite="mid:OFE29E2FA7.DBB108B6-ON852577D7.00772261-85257875.006F91C4@notes.cc.sunysb.edu" type="cite"><font size="2" face="sans-serif">Hello,</font> <br> <br> <font size="2" face="sans-serif">We just purchased a Zcorp 650, </font><a moz-do-not-send="true" href="http://www.zcorp.com/en/Products/3D-Printers/ZPrinter-650/spage.aspx"><font size="2" face="sans-serif">http://www.zcorp.com/en/Products/3D-Printers/ZPrinter-650/spage.aspx</font></a><font size="2" face="sans-serif"> and would like to begin building models of proteins. As you probably know, when you print a physical model of a protein @ 100,000x scale on one of these printers, it is very fragile. To help support the model, one must place "Struts" in key locations. </font> <br> <br> <font size="2" face="sans-serif">We currently use Jmol because it has a strut algorithm built into the software. The algorithm is open source, written originally by George Phillips and adapted by Bob Hanson (see email below). But Stony Brook faculty are begging us to train our students on Chimera and not JMol because (not surprisingly) most faculty at SBU use Chimera and not JMol.</font> <br> <br> <font size="2" face="sans-serif">My question: would you be willing to incorporate this algorithm into Chimera (or does it already exist)? This would allow Chimera to output pdb files that are ready for rapid prototyping, a blossoming field: </font><a moz-do-not-send="true" href="http://www.economist.com/node/18114327?story_id=18114327&CFID=162504503&CFTOKEN=65134946"><font size="2" face="sans-serif">http://www.economist.com/node/18114327?story_id=18114327&CFID=162504503&CFTOKEN=65134946</font></a> <br> <br> <font size="2" face="sans-serif">I look forward to your response,</font> <br> <font size="2" face="sans-serif">Marvin</font> <br> <br> <br> <font size="2" face="sans-serif">Marvin H. O'Neal III, Ph.D.<br> Undergraduate Biology<br> 108 CMM/BLL<br> Stony Brook University<br> Stony Brook, NY 11794-5110<br> Phone: (631) 632-1326<br> Fax: (631) 632-1680</font> <br> <br> <br> <font size="3">Sure, why not! It's not my algorithm, though. See </font><a moz-do-not-send="true" href="http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java"><font size="3" color="blue">http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/modelsetbio/AlphaPolymer.java</font></a><font size="3"><br> <br> 125 //<br> 126 // Struts calculation (for rapid prototyping)<br> 127 //<br> 128 ///////////////////////////////////////////////////////////<br> 129 /**<br> 130 *<br> 131 * Algorithm of George Phillips </font><a moz-do-not-send="true" href="mailto:phillips@biochem.wisc.edu"><font size="3" color="blue">phillips@biochem.wisc.edu</font></a><font size="3"><br> 132 *<br> 133 * originally a contribution to pyMol as struts.py;<br> 134 * adapted here by Bob Hanson for Jmol 1/2010<br> 135 *<br> 136 * Return a vector of support posts for rapid prototyping models<br> 137 * along the lines of George Phillips for Pymol except on actual molecular<br> 138 * segments (biopolymers), not PDB chains (which may or may not be<br> 139 * continuous).<br> <br> <br> Bob<br> </font> <br> <font size="3">On Thu, Apr 14, 2011 at 9:57 AM, <</font><a moz-do-not-send="true" href="mailto:moneal@notes.cc.sunysb.edu"><font size="3" color="blue">moneal@notes.cc.sunysb.edu</font></a><font size="3">> wrote:</font> <br> <font size="2" face="sans-serif">Bob,<br> <br> I teach introductory biology labs at Stony Brook and use physical models to introduce students to research. I have used Ras-Mol but recently switched to Chimera. I would like to share your strut algorithm with the Chimera group in hopes that they will incorporate it into the software.<br> <br> Would you be willing to work with me on this?<br> <br> Marvin<br> <br> Marvin H. O'Neal III, Ph.D.<br> Undergraduate Biology<br> G-05 CMM/BLL<br> Stony Brook University<br> Stony Brook, NY 11794-5110<br> Phone: </font><a moz-do-not-send="true" href="tel:%28631%29%20632-1326" target="_blank"><font size="2" color="blue" face="sans-serif">(631) 632-1326</font></a><font size="2" face="sans-serif"><br> Fax: </font><a moz-do-not-send="true" href="tel:%28631%29%20632-1680" target="_blank"><font size="2" color="blue" face="sans-serif">(631) 632-1680</font></a><font size="2" face="sans-serif"><br> </font><font size="2" color="#a1009f" face="sans-serif"><br> -----Forwarded by Marvin O'Neal/CAS on 04/14/2011 10:45AM -----</font> <br> <font size="2" face="sans-serif">To: </font><a moz-do-not-send="true" href="mailto:moneal@notes.cc.sunysb.edu" target="_blank"><font size="2" color="blue" face="sans-serif">"moneal@notes.cc.sunysb.edu"</font></a><font size="2" face="sans-serif"> </font><a moz-do-not-send="true" href="mailto:moneal@notes.cc.sunysb.edu" target="_blank"><font size="2" color="blue" face="sans-serif"><moneal@notes.cc.sunysb.edu></font></a><font size="2" face="sans-serif"><br> From: "Franzen, Margaret" </font><a moz-do-not-send="true" href="mailto:franzen@msoe.edu" target="_blank"><font size="2" color="blue" face="sans-serif"><franzen@msoe.edu></font></a><font size="2" face="sans-serif"><br> Date: 04/13/2011 01:56PM<br> Subject: RE: strut algorithm<br> (See attached file: Bob Hansen.vcf)<br> <br> </font><p><a moz-do-not-send="true" name="12f548420460d22e_Bob_Hansen"></a><font size="2" color="#004080" face="sans-serif">Hi, Marvin!</font> </p><div><font size="2" color="#004080" face="sans-serif"> </font> <br class="webkit-block-placeholder"></div><p><font size="2" color="#004080" face="sans-serif">Your earlier question now makes sense! Bob Hansen is the Jmol guru who teaches Chemistry at St. Olaf – and breathes life into all things Jmol. His contact is below:</font> </p><div><font size="2" color="#004080" face="sans-serif"> </font> <br class="webkit-block-placeholder"></div><p><span><mime-attachment.jpeg></span> </p><div><font size="2" color="#004080" face="sans-serif"> </font> <br class="webkit-block-placeholder"></div><p><font size="2" color="#004080" face="sans-serif">Margaret</font> </p><div><font size="2" color="#004080" face="sans-serif"> </font> <br class="webkit-block-placeholder"></div><p><font size="2" face="sans-serif">From: </font><a moz-do-not-send="true" href="mailto:moneal@notes.cc.sunysb.edu" target="_blank"><font size="2" color="blue" face="sans-serif">moneal@notes.cc.sunysb.edu</font></a><font size="2" face="sans-serif"> [</font><a moz-do-not-send="true" href="mailto:moneal@notes.cc.sunysb.edu" target="_blank"><font size="2" color="blue" face="sans-serif">mailto:moneal@notes.cc.sunysb.edu</font></a><font size="2" face="sans-serif">] <br> Sent: Wednesday, April 13, 2011 12:51 PM<br> To: Franzen, Margaret<br> Subject: RE: strut algorithm</font> </p><div><font size="2" face="sans-serif"> </font> <br class="webkit-block-placeholder"></div><p><font size="2" face="sans-serif">Hey Margaret,</font> </p><div><font size="2" face="sans-serif"> </font> <br class="webkit-block-placeholder"></div><p><font size="2" face="sans-serif">My question about the Strut command in Jmol was specific to the math of the algorithm. I was looking for the equation that runs in the background when a student types this command. I couldn't find it in the documentation guide.</font> </p><div><font size="2" face="sans-serif"> </font> <br class="webkit-block-placeholder"></div><p><font size="2" face="sans-serif">Do you have Bob's email? There seem to be several Bob Hanson's on the internet.</font> </p><div><font size="2" face="sans-serif"> </font> <br class="webkit-block-placeholder"></div><p><font size="2" face="sans-serif">Marvin<br> <br> Marvin H. O'Neal III, Ph.D.<br> Undergraduate Biology<br> G-05 CMM/BLL<br> Stony Brook University<br> Stony Brook, NY 11794-5110<br> Phone: </font><a moz-do-not-send="true" href="tel:%28631%29%20632-1326" target="_blank"><font size="2" color="blue" face="sans-serif">(631) 632-1326</font></a><font size="2" face="sans-serif"><br> Fax: </font><a moz-do-not-send="true" href="tel:%28631%29%20632-1680" target="_blank"><font size="2" color="blue" face="sans-serif">(631) 632-1680</font></a> </p><div> <br class="webkit-block-placeholder"></div> <pre wrap=""><fieldset class="mimeAttachmentHeader"></fieldset>
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