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Hi Dialing,<br>
<br>
H geometry should be ideal after phenix.refine. If it is not the
case then please send me the PDB and I will have a look.<br>
<br>
Pavel<br>
<br>
On 12/6/11 3:49 AM, Dialing Pretty wrote:
<blockquote
cite="mid:1323172146.66075.YahooMailNeo@web121715.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<div>Dear All,</div>
<div><br>
</div>
<div>I did a Phenix refine, and before the refine all the H were
added. MolProbity analysis demonstrated that almost everything
are acceptable after the refinement.</div>
<div><br>
</div>
<div>However when I did the geometry analysis by the COOT
validation, I find all the residues having a significant
deviation bond involving H. with z score higher than 7.</div>
<div><br>
</div>
<div>I am looking forward to getting an explanation from you on
it,including how to avoid it.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Dialing</div>
</div>
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