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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