[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?
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.
>
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