<div dir="ltr">Zhijie<div><br></div><div style>I have fixed both these bugs and you should be able to download the next nightly build to run ReadySet! on your file. In the meantime, I'm happy to run ReadySet! on your model. Make sure you send it off list.</div>
<div style><br></div><div style>Nigel</div><div style><br></div><div style>NB. Any files sent to me will be held in strictest confidence.<br><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Apr 29, 2013 at 4:42 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">Hi Nigel,</font></div>
<div><font face="Arial"></font>�</div>
<div><font face="Arial">Please find the two attached PDB files. One is
before ReadySet, the other after.</font></div>
<div><font face="Arial"></font>�</div>
<div><font face="Arial">Zhijie</font></div>
<div style="FONT:10pt Tahoma">
<div><br></div>
<div style="BACKGROUND:#f5f5f5">
<div><b>From:</b> <a title="nwmoriarty@lbl.gov" href="mailto:nwmoriarty@lbl.gov" target="_blank">Nigel Moriarty</a> </div>
<div><b>Sent:</b> Monday, April 29, 2013 7:36 PM</div>
<div><b>To:</b> <a title="phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org" target="_blank">PHENIX user mailing list</a> </div>
<div><b>Subject:</b> Re: [phenixbb] ReadySet & phenix.refine problem:
NAG-Asn with hydrogen atoms</div></div></div><div><div class="h5">
<div><br></div>
<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="PADDING-LEFT:1ex;MARGIN:0px 0px 0px 0.8ex;BORDER-LEFT:#ccc 1px solid"><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><font color="#888888">
<div>�</div></font></span></font></div><span><font color="#888888">
<div><font face="Arial">Zhijie</font></div></font></span></div><br>_______________________________________________<br>phenixbb
mailing list<br><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
<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 : <a href="tel:510-486-5709" value="+15104865709" target="_blank">510-486-5709</a>� �� Email :
NWMoriarty@LBL.gov<br>Fax�� : <a href="tel:510-486-5909" value="+15104865909" target="_blank">510-486-5909</a>� � ��
Web� : <a href="http://CCI.LBL.gov" target="_blank">CCI.LBL.gov</a> </div>
</div></div><p>
</p><hr><div class="im">
<p></p>_______________________________________________<br>phenixbb mailing
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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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