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Hi Georg,<br>
<br>
I think the refinement .log file should contain the lines like these
below:<br>
<br>
Warning: very small nonbonded interaction distances.<br>
Nonbonded interactions: 12604<br>
Sorted by model distance:<br>
nonbonded pdb=" CG ARG A 3 "<br>
pdb=" CG ARG A 4 "<br>
model vdw<br>
0.000 3.840<br>
nonbonded pdb=" NE ARG A 3 "<br>
pdb=" NE ARG A 4 "<br>
model vdw<br>
0.000 3.200<br>
<br>
which pinpoints you the offending atoms. <br>
<br>
Does this answer your question?<br>
<br>
Pavel.<br>
<br>
On 1/19/10 9:57 AM, Georg Mlynek wrote:
<blockquote
cite="mid:001c01ca9930$dbbc2160$93346420$%25mlynek@univie.ac.at"
type="cite">
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<title>clash guarde failure phenix coot</title>
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<p dir="ltr"><span lang="de-at"></span><span lang="en-us"><font
face="Consolas">Dear All,</font></span><span lang="de-at"></span><span
lang="en-us"> </span></p>
<p dir="ltr"><span lang="de-at"></span><span lang="en-us"><font
face="Consolas">I´m refining a 2.1A</font></span><span lang="de-at"></span><span
lang="en-us"> <font face="Consolas">with phenix 1.5-2 and get</font></span><span
lang="de-at"></span><span lang="en-us"> <font face="Consolas">when I
click on automatically add hydrogens to model</font></span><span
lang="de-at"></span><span lang="en-us"> <font face="Consolas">following</font></span><span
lang="de-at"></span><span lang="en-us"><font face="Consolas"> error
message:</font></span><span lang="de-at"></span><span lang="en-us"> <font
face="Consolas">refinement</font></span><span lang="de-at"></span><span
lang="en-us"><font face="Consolas">.</font></span><span lang="de-at"></span><span
lang="en-us"><font face="Consolas">pdb_interpretation.clash_guard.failure:
Number of nonbonded interaction distances <</font></span><span
lang="de-at"></span><span lang="en-us"></span><span lang="de-at"></span><span
lang="en-us"> <font face="Consolas">0.5:391</font></span><span
lang="de-at"></span><span lang="en-us"></span></p>
<p dir="ltr"><span lang="de-at"></span><span lang="en-us"></span></p>
<p dir="ltr"><span lang="en-us"><font face="Consolas">I suppose that
this comes, because coo</font></span><span lang="de-at"></span><span
lang="en-us"><font face="Consolas">t mixes up the hydrogens. </font></span></p>
</blockquote>
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