[phenixbb] clash guarde failure phenix coot

Pavel Afonine PAfonine at lbl.gov
Tue Jan 19 10:38:15 PST 2010

Hi Georg,

I think the refinement .log file should contain the lines like these below:

  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 12604
  Sorted by model distance:
  nonbonded pdb=" CG  ARG A   3 "
            pdb=" CG  ARG A   4 "
     model   vdw
     0.000 3.840
  nonbonded pdb=" NE  ARG A   3 "
            pdb=" NE  ARG A   4 "
     model   vdw
     0.000 3.200

which pinpoints you the offending atoms.

Does this answer your question?


On 1/19/10 9:57 AM, Georg Mlynek wrote:
> Dear All,
> I´m refining a 2.1A with phenix 1.5-2 and get when I click on 
> automatically add hydrogens to model following error message: 
> refinement.pdb_interpretation.clash_guard.failure: Number of nonbonded 
> interaction distances < 0.5:391
> I suppose that this comes, because coot mixes up the hydrogens.
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