[phenixbb] a command on Phenix refine
Pavel Afonine
pafonine at lbl.gov
Sun Jan 4 11:25:10 PST 2015
Hello,
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
refinement.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
into a file and give this file to phenix.refine along with all other
file (PDB, reflections, etc).
Pavel
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
>
>
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