[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 

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,

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