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<DIV><FONT face=Arial size=2>Hi Nigel,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Please find the two attached PDB files. One is
before ReadySet, the other after.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Zhijie</FONT></DIV>
<DIV style="FONT: 10pt Tahoma">
<DIV><BR></DIV>
<DIV style="BACKGROUND: #f5f5f5">
<DIV style="font-color: black"><B>From:</B> <A title=nwmoriarty@lbl.gov
href="mailto:nwmoriarty@lbl.gov">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">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><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 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><BR>_______________________________________________<BR>phenixbb
mailing list<BR><A
href="mailto:phenixbb@phenix-online.org">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 : 510-486-5709 Email :
NWMoriarty@LBL.gov<BR>Fax : 510-486-5909
Web : <A href="http://CCI.LBL.gov">CCI.LBL.gov</A> </DIV>
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