[Chimera-users] Trying to change dihedrals: ValueError: bond is part of a cycle

Nikolaos Bismpikos nikolaosbismpikos at gmail.com
Mon Jun 26 11:31:48 PDT 2017

Hey, my goal is to change the dihedrals of an already existing pdb template
in order to find low-energy protein conformations.

The issue I have here is that for some residues the dihedrals phi and psi
cannot be changed. That's the error I get:

Traceback (most recent call last):
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line
683, in init
    chimera.openModels.open(a, prefixableType=1)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py",
line 1929, in open
    models = func(filename, *args, **kw)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py",
line 1299, in _openPython
    loadFunc(sandboxName, fileName, f)
  File "predictor.py", line 40, in <module>
  File "/home/nick/Python/pdb/AbstractOptimizer.py", line 97, in main_loop
    self.fs, self.evals, self.terminate =
  File "/home/nick/Python/pdb/eval_energy.py", line 20, in eval_energy
    allR[j].phi = pop[i,j];
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py",
line 98, in setPhi
    _setAngle(bond, phi, getPhi(res, missingIsError=True), "phi",
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py",
line 147, in _setAngle
    br = BondRot(bond)
ValueError: bond is part of a cycle

Is there a way to determine beforehand which bonds are part of circle and
hence which residues' dihedral information cannot be changed?

Thank you in advanced for your time,

Nikolaos Bismpikos
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