[phenixbb] Max_reasonble_bond_distance error in phene.resl.space.refine

Rune Thomas Kidmose rtk at mbg.au.dk
Tue Nov 14 13:16:51 PST 2017

Hi Again Pavel,

I should add that this (see download link for PDB file) is how the the same PDB file (last_frame.pdb from last email) looks when I have put it through phenix.RSR

PDB: https://www.dropbox.com/s/ectbydhsh1fx7dh/last_frame_rsr.pdb?dl=0

The protein part of the model behaves really well, as I normally see when using phenix.RSR, however the DNA seems to move much more random, almost uncoiling.

This is why I stated that the quality of the refinement seemed to suffer from the increase max bond distance. But again, I am using phenix dev-2614 so maybe that has something to do with it.



Fra: Pavel Afonine <pafonine at lbl.gov>
Sendt: 14. november 2017 16:20
Til: Rune Thomas Kidmose; phenixbb at phenix-online.org
Emne: Re: [phenixbb] Max_reasonble_bond_distance error in phene.resl.space.refine

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,

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