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Hi Lu,<br>
<br>
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cite="mid:2c4c950b.52c7.14e9a01752b.Coremail.luzuokun@126.com"
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<div> The serine contains no H atoms and the ligand has H
atoms in the PDB file. How do Phenix refine deal with this two
kind of H atoms at nearly the same place?<br>
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<br>
phenix.refine is a refinement program, not model building. It will
attempt to refine whatever you give it, good or garbage, and, in
case of garbage in, expect garbage out, typically.<br>
<br>
So if you have that H that given the new bond should go, then you
should delete it. Perhaps we should detect such cases automatically
and deal with them seamlessly (thoughts, Nigel?) but at present it
appears to me as the next level of sophistication that we haven't
gotten to yet.<br>
<br>
<blockquote
cite="mid:2c4c950b.52c7.14e9a01752b.Coremail.luzuokun@126.com"
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<div>I have deleted the H atoms of the ligand, and refined
again. The coordinate is reasonable without H atoms being
seen. <br>
So, I think the simplest way is to delete all H atom in such
resolution.<br>
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<br>
Yes, this is true.<br>
<br>
<blockquote
cite="mid:2c4c950b.52c7.14e9a01752b.Coremail.luzuokun@126.com"
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<div>Best wishes!<br>
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<br>
Likewise!<br>
<br>
Pavel<br>
<br>
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