[phenixbb] a command on Phenix refine

Pavel Afonine pafonine at lbl.gov
Sun Jan 4 11:25:10 PST 2015


this error means your input PDB file contains atoms that nearly 
perfectly overlap. It is best if you inspect the PDB file and resolve 
the issues.

Answering your question:

In phenix.refine GUI :

Refinement settings -> All parameters -> Search parameters

paste nonbonded_distance_threshold and hit Enter. In popped window 
replace default 0.5 with an empty line and save.

Alternatively, you can save one line


into a file and give this file to phenix.refine along with all other 
file (PDB, reflections, etc).


On 1/1/15 7:22 PM, Wind Sui wrote:
> Dear All,
> I use the graphic phenix.refine to do a refinement, and Phenix 
> informed me I need to have a command 
> "refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None". 
> Will you please tell me by graphic phenic.refine, how can I input this 
> command?
> Wind
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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