<FONT face="Default Sans Serif,Verdana,Arial,Helvetica,sans-serif" size=2><div>Just a thought, but running the default "phenix.refine" command is going to refine individual atomic coordinates and ADPs, unless you specify otherwise. At 3.3A are you sure you have enough data to model all of these parameters? Even with heavy restraints, i'm not sure individual coordinate refinement is feasible. Perhaps doing a rigid-body refinement of multiple groups with grouped ADPs would yield better results. You could even model in TLS groups. </div><div><br></div><div>From what I understand, if you regularize the geometry before refinement as Pavel suggested, the side-chains shouldn't move back to outlier regions, since the side-chains will not be refined in rigid-bodies.</div><div><br></div><div>Just a friendly thought :) </div><div><br></div><div>Best wishes,</div><div><br></div><div>Jason Porta<br>Graduate Student</div><div>Eppley Structural Biology Facility<br>Dept. Biochemistry & Molecular Biology<br>University of Nebraska Medical Center<br>Omaha, NE 68198<br>(402) 559-5533<br><div><br></div><font color="#990099">-----phenixbb-bounces@phenix-online.org wrote: -----<br><br></font><blockquote style="padding-right:0px;padding-left:5px;margin-left:5px;border-left:#000000 2px solid;margin-right:0px">To: "PHENIX user mailing list" <phenixbb@phenix-online.org><br>From: "guanrj@foxmail.com" <guanrj@foxmail.com><br>Sent by: phenixbb-bounces@phenix-online.org<br>Date: 04/14/2010 12:00PM<br>Subject: Re: [phenixbb] Phenix.refine bonds/angles rmsd<br><br>
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<div><font face="宋体" size="2"><font face="Times New Roman"><font size="3">Thank you
very much for your suggestions. I will try all these options and let you
know</font></font></font></div>
<div><font face="宋体" size="2"><font face="Times New Roman"><font size="3">the results.
</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">Rongjin
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<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>2010-04-14 12:03:10 You
wrote <font color="#666666">= = = = = = = = </font></font></font></div>
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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><br>
<blockquote cite="mid:201004141009505787450@foxmail.com" type="cite">
<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></blockquote><br>you may want to
consider:<br><br>- using secondary structure restraints;<br>- tightening
restraints (using wxc_scale=...);<br>- using H atoms in refinement;<br>-
doing some quick geometry regularization before refinement;<br>- fixing
manually and excluding from refinement certain parts of your
model.<br><br>You need to experiment and find empirically which
combination of the above options works in your case. I would appreciate
if you share your experience with this and tell us what worked for your
in the
end.<br><br>Pavel.<br><br></blockquote></td></tr></tbody></table></font></div></div>
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