[phenixbb] clash_guard failure

Pavel Afonine pafonine at lbl.gov
Wed Apr 20 22:48:19 PDT 2016


Hi Todias,

it's hard to diagnose this without seeing the files. Could you please 
send me relevant files so that I can run refinement myself and reproduce 
the crash?

Pavel

On 4/20/16 22:40, Bock, Tobias wrote:
>
> Dear colleagues,
>
> I am trying to refine a protein-DNA complex. In this structure, 2 DNA 
> double strands are present with 50% occupancy (or similar occupancy’s) 
> and overlap at certain positions. Phenix.refine crashed  due to a 
> nonbonded interaction distance issue. To fix that, I tried to exclude 
> the DNA strands using:
>
> *pdb_interpretation {
>  custom_nonbonded_symmetry_exclusions="chain E"
>  custom_nonbonded_symmetry_exclusions="chain F"
>  }*
>
> Nevertheless, phenix.refine crashed with the same error message. 
> Changing the “*nonbonded_distance_threshold*” works, but results in 
> terrible statistics (since this applies for the complete structure, I 
> guess).
>
> Is there a way to exclude only the DNA strands (in regard to the clash 
> guard) or a similar approach to refine the structure?
>
> Thank you in advance for your help,
>
> Tobias
>
>
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