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

Pavel Afonine pafonine at lbl.gov
Wed Nov 15 09:03:23 PST 2017


Hi All,

just in case somebody else had similar problems: it seems that using a 
recent Phenix version 1.13rc1 (2954) fixes the 
max_reasonable_bond_distance issue (at least in the reported by Ruki cases).

Pavel

On 11/14/17 13:16, Rune Thomas Kidmose wrote:
>
> 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.
>
>
> Cheers
>
> Ruki
>
>
>
>
> ------------------------------------------------------------------------
> *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,
> Pavel
>

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