<div dir="ltr">Can you send me the ASN-NAG PDB file?</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Apr 29, 2013 at 4:01 PM, Zhijie Li <span dir="ltr"><<a href="mailto:zhijie.li@utoronto.ca" target="_blank">zhijie.li@utoronto.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><u></u>
<div style="PADDING-RIGHT:10px;PADDING-LEFT:10px;PADDING-TOP:15px" name="Compose message area">
<div><font face="Arial">Hello,</font></div>
<div><font face="Arial"></font>�</div>
<div><font face="Arial">I am refining my structure with hydrogen atoms on
(phenix 1.8.2-1309). The protein contains two Asn-linked GlcNAc. I noticed two
problems with respect to the NAG-Asn linkage in the presence of hydrogen
atoms:</font></div>
<div><font face="Arial"></font>�</div>
<div><font face="Arial">1) After running ReadySet (to add hydrogen to the
PDB <em>ab initio</em>), the H1 on the NAG is pointing to the amino group of
Asn, ie, the NAG seems to be interpreted�as in�its alpha anomer
instead of beta (should be GlcNAc beta1,N-Asn).�This is not really a
problem as it doesn't seem to affect the refinement.</font></div>
<div><font face="Arial"></font><font face="Arial"></font>�</div>
<div><font face="Arial">2) The H21 in Asn is correctly removed�by
ReadySet, leaving only H22. However, if I send this PDB to phenix.refine, the
refinement will fail almost instantly complaining that H22 of the Asn has an
unknown nonbonded energy type symbol. But if I simply change the atom name of
H22 to H21, the refinement will�proceed to completion with no problem, only
leaving an H21�at the position where H22 should be.</font></div>
<div><font face="Arial"></font><font face="Arial"></font>�</div>
<div><font face="Arial">I�was not sure what caused this error. So I
trimmed my PDBs down to the Asn and NAG only, and fed the small PDB to ReadySet
and phenix.refine (with an eff file indicating the NAG-Asn linkage) and got the
same behavior: H22 on Asn - error; H21 on Asn -�OK. </font></div>
<div><font face="Arial"></font>�</div>
<div><font face="Arial">
<div><font face="Arial">I hope someone can look into this. Thanks in
advance.</font></div><span class="HOEnZb"><font color="#888888">
<div>�</div></font></span></font></div><span class="HOEnZb"><font color="#888888">
<div><font face="Arial">Zhijie</font></div></font></span></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709� �� Email : NWMoriarty@LBL.gov<br>
Fax�� : 510-486-5909� � �� Web� : <a href="http://CCI.LBL.gov">CCI.LBL.gov</a>
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