[phenixbb] non-bonded

Pavel Afonine pafonine at lbl.gov
Thu Jan 23 13:59:07 PST 2014


this means the PDB file that you gave to phenix.refine contains atoms 
that perfectly (within 0.0001) overlap. If that's what you want, then 
just follow what phenix.refine suggests to keep going (I think it prints 
out a keyword that disables this error message). Otherwise edit  PDB 
file and run refinement again.

If this does not help please send me PDB file.


On 1/23/14, 12:31 PM, Leonard Thomas wrote:
> Hello All,
> We are trying to refine a complex that was solved using Phaser.  We 
> have run a round of rigid body refinement using Refmac and now want to 
> run a simulated annealing run in Phenix.  Visually the complex looks 
> pretty.  The resolution we currently are at is 3.6 A.  When we go to 
> run phenix.refine the program quits with a Number of non-bonded 
> interactions < 0.0001 error.  Is there a way to loosen this up a bit 
> or get around it or should we go about this in a different way?
> Best Regard,
> Leonard Thomas, Ph.D.
> Macromolecular Crystallography Laboratory Manager
> University of Oklahoma
> Department of Chemistry and Biochemistry
> Stephenson Life Sciences Research Center
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office: (405)325-1126
> lmthomas at ou.edu <mailto:lmthomas at ou.edu>
> http://barlywine.chem.ou.edu
> http://structuralbiology.ou.edu
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