<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Carlos,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I think you are going to have to resort to Python here. First, look at this page for a basic example of how to loop over some files and do something with them in Chimera/Python:</div><div class=""><br class=""></div><div class=""><a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html" class="">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a></div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You form the C-N peptide bond using the <i class="">cnPeptideBond</i> function from the <i class="">BuildStructure</i> module. Here’s a pseudocode fragment to form the bond:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>runCommand(“sel atom-spec-to-select-the-N-and-the-C”)</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>from chimera.selection import currentAtoms</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>n, c = currentAtoms()</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>if n.element.name != “N”:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span># the atoms were in the other order, swap them</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>n, c = c, n</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>from BuildStructure import cnPeptideBond</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>cnPeptideBond(c, n, c, 1.33, 180.0, phi=-120.0)</div><div class=""><br class=""></div><div class="">You might want to put the above in yet another loop so that you could try various phi angles. Naturally you would have to break the bond before trying another value, probably with the ~bond command.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>You might also want to directly measure the clashes in the script rather than write them out to a file. You do that with the <i class="">detectClash</i> function in the <i class="">DetectClash</i> module. Here’s more pseudocode:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>runCommand(“sel atom-spec to select the C-terminal tail”)</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>from chimera.selection import currentAtoms</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>from DetectClash import detectClash</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>num_clashing_atoms = len(detectClash(currentAtoms()))</div><div class=""><br class=""></div><div class="">Good luck!</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><br class=""><div apple-content-edited="true" class="">
<div style="color: rgb(0, 0, 0); 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 class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><br class=""></div><div><blockquote type="cite" class=""><div class="">On Oct 6, 2015, at 1:49 PM, Carlos Gonzalez Oliver, Mr <<a href="mailto:carlos.gonzalezoliver@mail.mcgill.ca" class="">carlos.gonzalezoliver@mail.mcgill.ca</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Dear Chimera,
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<div class="">I have been trying to use Join Models to make a C-N bond between the globular domain of a protein and a region of it (a C-terminal tail) whose structure I simulated using MD.</div>
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<div class="">However, when I do the joining with Join Models C-N bond option, I get some serious steric clashes. I have tried to resolve them by hand by adjusting the bond's torsion and angles but it is too complicated.</div>
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<div class="">Other than trying to use other software to minimize clashes, I think I might have to use a brute force method and try a bunch of the structures my MD generated until one of them works.</div>
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<div class="">So what I am trying to do now is write a script to do the model joining automatically with many different structures that I generated, and return the one with the least number of clashes.</div>
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<div class="">But I haven't been able to find a command line equivalent of the Join Models window.. I was wondering if you know if such a command exists, if not what combination of commands would work? (for repositioning the models and forming the bond)</div>
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<div class="">Thanks!</div>
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<div class="">--</div>
<div class="">Carlos G. Oliver</div>
<div class="">M.Sc. Student</div>
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<div class="">Vogel Lab</div>
<div class="">Department of Biology</div>
<div class="">McGill University</div>
<div class="">Montréal, QC, Canada</div>
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