<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 Nikolaos,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera doesn’t store that information, so there’s no direct way to find out. Obviously, you could loop through your residues beforehand and do “r.phi = r.phi” and catch ValueError to mark the residues involved in cycles.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>The other option is to edit phipsi.py in /home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera and in the setPhi and setPsi functions add ValueError to the list of errors that it ignores.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div 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><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Jun 26, 2017, at 11:31 AM, Nikolaos Bismpikos <<a href="mailto:nikolaosbismpikos@gmail.com" class="">nikolaosbismpikos@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Hey, my goal is to change the dihedrals of an already existing pdb template in order to find low-energy protein conformations.<br class=""><br class=""></div>The issue I have here is that for some residues the dihedrals phi and psi cannot be changed. That's the error I get:<br class=""><br class="">Traceback (most recent call last):<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init<br class=""> chimera.openModels.open(a, prefixableType=1)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open<br class=""> models = func(filename, *args, **kw)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython<br class=""> loadFunc(sandboxName, fileName, f)<br class=""> File "predictor.py", line 40, in <module><br class=""> es.main_loop();<br class=""> File "/home/nick/Python/pdb/AbstractOptimizer.py", line 97, in main_loop<br class=""> self.fs, self.evals, self.terminate = self.eval_pop(self.eval_func,self.pop,self.evals,self.eval_budget,self.extra_par)<br class=""> File "/home/nick/Python/pdb/eval_energy.py", line 20, in eval_energy<br class=""> allR[j].phi = pop[i,j];<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 98, in setPhi<br class=""> _setAngle(bond, phi, getPhi(res, missingIsError=True), "phi", anchorSide)<br class=""> File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 147, in _setAngle<br class=""> br = BondRot(bond)<br class="">ValueError: bond is part of a cycle<br class=""><br class=""><br class=""></div>Is there a way to determine beforehand which bonds are part of circle and hence which residues' dihedral information cannot be changed?<br class=""><br class=""></div>Thank you in advanced for your time,<br class=""><br class=""></div>Nikolaos Bismpikos<br class=""></div>
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