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

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 26 11:55:03 PDT 2017


Hi Nikolaos,
	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.
	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.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jun 26, 2017, at 11:31 AM, Nikolaos Bismpikos <nikolaosbismpikos at gmail.com> wrote:
> 
> 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>
>     es.main_loop();
>   File "/home/nick/Python/pdb/AbstractOptimizer.py", line 97, in main_loop
>     self.fs, self.evals, self.terminate = self.eval_pop(self.eval_func,self.pop,self.evals,self.eval_budget,self.extra_par)
>   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", anchorSide)
>   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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