Hi Len, Can't you re-run rigid body in Phenix and feed it directly to SA? Just trying to stay involved, feel free to ignore me.... :) On Thursday, January 23, 2014 3:59 PM, Pavel Afonine wrote: Hello, 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. Pavel 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 73019-5251Office: (405)325-1126

[email protected] http://barlywine.chem.ou.edu http://structuralbiology.ou.edu

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