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<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT size=3>Hi
Pavel</FONT></FONT></FONT></DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT
size=3></FONT></FONT></FONT> </DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT size=3>Thanks for
your suggestion. I have another question:</FONT></FONT></FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">I am refining another 3.3 A resolution
structure. In coot I manually adjusted the model</FONT></DIV>
<DIV><FONT face="Times New Roman">to have >95% residues in preferred
region in ramanchandran plot, but after refinement </FONT></DIV>
<DIV><FONT face="Times New Roman">in Phenix only </FONT><FONT
face="Times New Roman"><80% residues in the preferred region and a lot more
in the outlier region.</FONT></DIV>
<DIV><FONT face="Times New Roman">This was wen I used the default refinement
parameters "phenix.refine mtz_file pdb_file".</FONT></DIV>
<DIV><FONT face="Times New Roman">R and R_free are 0.22/0.27 in this case.
</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">Then when I used "phenix.refine mtz_file
pdb_file wxc_scale=0.1 wxu_scale=0.3", I can </FONT></DIV>
<DIV><FONT face="Times New Roman">get better results in terms of ramanchandran
plot (say, ~92% in preferred region, and a</FONT></DIV>
<DIV><FONT face="Times New Roman">little more in the outlier). <FONT
face="Times New Roman">R and R_free factors are
0.25/0.30.</FONT></FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">I guess at low resolution (like in my case,
3.3 A) I have to give more weights to geometry </FONT></DIV>
<DIV><FONT face="Times New Roman">restrains. Did I do it in the right way, or
did I missing anything?</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">Thanks</FONT></DIV>
<DIV><FONT face="Times New Roman"></FONT> </DIV>
<DIV><FONT face="Times New Roman">Rongjin Guan </FONT></DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT
size=3></FONT></FONT></FONT> </DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT
size=3></FONT> </DIV>
<DIV><FONT face=宋体 size=2></FONT> </DIV>
<DIV><FONT face=宋体 size=2></FONT> </DIV></FONT></FONT>
<DIV><FONT size=2><FONT face="Times New Roman"><FONT color=#666666>= = = = = = =
= <FONT color=#000000>On </FONT></FONT>2010-04-13 16:42:21 You
wrote <FONT color=#666666>= = = = = = = = </FONT></FONT></FONT></DIV>
<DIV><FONT face="Times New Roman" size=2>
<TABLE width="100%">
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<BLOCKQUOTE
style="PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">Hi
Rongjin,<BR>
<BLOCKQUOTE cite=mid:201004131728171257643@foxmail.com
type="cite"><FONT face=Verdana size=2>
<DIV>when I use phenix.refine to refine my structure, the rmsd's
of bonds and angles are </DIV>
<DIV>pretty large. My data is 2.3 A resolution. </DIV>
<DIV> </DIV>
<DIV>REMARK<BR>REMARK ******************** REFINEMENT SUMMARY: QUICK
FACTS *******************<BR>REMARK Start: r_work = 0.2838 r_free =
0.2789 bonds = 0.029 angles = 2.002<BR>REMARK Final: r_work = 0.2407
r_free = 0.2466 bonds = 0.029 angles = 2.002<BR>REMARK
************************************************************************<BR>REMARK<BR></DIV></FONT></BLOCKQUOTE><BR>really
(just wondering)? <BR>What I would be really worry is the difference
between Rfree and Rwork, which apparently is terribly small, indicating
that there is something wrong with either free-R flags or refinement
strategy.<BR><BR>
<BLOCKQUOTE cite=mid:201004131728171257643@foxmail.com
type="cite"><FONT face=Verdana size=2>
<DIV>I tried many options but none worked so far. Here are the
options that I tried:</DIV>
<DIV> </DIV>
<DIV>phenix.refine mtz_file pdb_file strategy=tls
tls_group_selections.params wxc_scale=0.3 wxu_scale=0.8</DIV>
<DIV> </DIV>
<DIV>phenix.refine mtz_file pdb_file strategy=tls
tls_group_selections.params fix_wxc=0.3 fix_wxu=0.8 </DIV>
<DIV> </DIV>
<DIV>phenix.refine mtz_file pdb_file strategy=tls
tls_group_selections.params fix_wxc=0.3 fix_wxu=0.8
optimize_wxc=false optimize_wxu=false</DIV>
<DIV> </DIV>
<DIV>These gave the same refinement results. Any
suggestions?</DIV></FONT></BLOCKQUOTE><BR>It's not surprising, because
in all refinements above you did not refine the coordinates at all. The
keyword "strategy=tls" means you refined B-factors only (more precisely,
you did constrained anisotropic refinement, called TLS refinement). And
therefore using wxc_scale or fix_wxc or optimize_wxc would not
make any difference. Also, optimize_wxc is set to False by default, so
you don't need to explicitly say it.<BR><BR>I would run it like
this:<BR><BR>phenix.refine mtz_file pdb_file
strategy=tls+individual_adp+individual_sites tls_group_selections.params
optimize_wxc=true<BR><BR>and hope that this fixes the
"problem".<BR><BR>Let me know if you have any
questions!<BR>Pavel.<BR><BR></BLOCKQUOTE></TD></TR></TBODY></TABLE></FONT></DIV></DIV></BODY></HTML>