[phenixbb] Max_reasonble_bond_distance error in phene.resl.space.refine
Pavel Afonine
pafonine at lbl.gov
Tue Nov 14 07:20:01 PST 2017
Hi Ruki,
> 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
there.
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
> max_reasonable_distance_error.
>
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,
Pavel
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