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? Pavel. 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.