[phenixbb] Max_reasonble_bond_distance error in phene.resl.space.refine
pafonine at lbl.gov
Tue Nov 14 07:20:01 PST 2017
> I have been playing around with phenix.real.space.refine as part of a
> small pipeline I am making for EM structures.
> Testing various deposited EM structures and their corresponding
> maps, within my pipeline, I sometimes run in to the below error:
> RuntimeError: Bond distance > max_reasonable_bond_distance: 79.8663 > 50:
I'm trying to chase this down and eliminate. So if you come across a
case that can be reproduced please send it to me and I will start from
For now simply set "max_reasonable_bond_distance=999" for all your
refinements that will mask but not fix the problem. However, this should
not affect the refinement results.
Make sure you are using the latest Phenix version.
> Followed by a list of distances between, what I am assuming is, atom
> numbers and the actual distance.
> I can get past it simply by changing
> the max_reasonable_bond_distance for the run to, in this case, 80.
This happens because the procedure optimizes weights by trying a large
sample of possible weight values. For some values restraints may be too
weak and atoms run one onto another, thus creating a huge clash and
strong repulsion that stretches the bond. This leads to the crash.
> But I tend to see, that the final results gets significantly worse
> when I use this bypass.
> This is based on very similar models going through the pipeline, where
> the ones which yields the error, scores much worse when using the
> above mentioned bypass, compared to the models that showed no
Again, I'm very keep to investigate concrete reproducible cases. So if
you have anything to share that would be most helpful!
> B: Any ide what I can do, to avoid running into this bond
> distance problem?
I'd say help us to identify the issue so that we fix it and then you
don't run into it any more.
All the best,
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