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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>
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<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT size=3>can you show me how to select some residues that are excluded from refinement?</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>You suggested this earlier but I did not know how to do it. I looked through the</FONT></FONT></FONT></DIV>
<DIV><FONT face=宋体 size=2><FONT face="Times New Roman"><FONT size=3>manual and I can see how to select a chain, but do not know how to select some residues</FONT></FONT></FONT><FONT face="Times New Roman">. </FONT></DIV>
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<DIV><FONT face="Times New Roman">Thanks</FONT></DIV>
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<DIV><FONT face="Times New Roman">Rongjin </FONT><FONT face=宋体 size=2><FONT face="Times New Roman"></DIV>
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<DIV id=menu_sender><B>From: </B> "Pavel Afonine"<PAfonine@lbl.gov>;</DIV>
<DIV><B>Date: </B> Thu, Apr 15, 2010 08:08 AM</DIV>
<DIV><B>To: </B> "PHENIX user mailing list"<phenixbb@phenix-online.org>; </DIV>
<DIV></DIV>
<DIV><B>Subject: </B> Re: [phenixbb] Real Space Refinement with marginal data</DIV></DIV>
<DIV> </DIV>Hi Carsten,<BR><BR>
<BLOCKQUOTE cite=mid:204D6E1BD9ACEA40B3F76FE9C125528F044023E7@JNJUSSHGMS01.na.jnj.com type="cite">
<P dir=ltr><SPAN lang=en-us><FONT face=Calibri>I was wondering if anyone had experience/advice for real space refinement with phenix using marginal data to 3A.</FONT></SPAN><SPAN lang=en-us> <FONT face=Calibri>I just did a run (SA, real-space refinement</FONT></SPAN><SPAN lang=en-us><FONT face=Calibri> against diff_map</FONT></SPAN><SPAN lang=en-us><FONT face=Calibri>, 2 fold NCS, grouped APD</FONT></SPAN><SPAN lang=en-us><FONT face=Calibri>, fix_rotamers enabled</FONT></SPAN><SPAN lang=en-us><FONT face=Calibri>)</FONT></SPAN><SPAN lang=en-us> <FONT face=Calibri>were the resulting structure showed lots of disconnected sidechains and some broken main chains.</FONT></SPAN><SPAN lang=en-us> <FONT face=Calibri>I am just repeating the run w/o real space refinement,</FONT></SPAN><SPAN lang=en-us><FONT face=Calibri> may be the combination of SA and real space refinement was a bit harsh,</FONT></SPAN><SPAN lang=en-us> <FONT face=Calibri> but am wondering what kind of parameters make most sense to tweak in order to avoid</FONT></SPAN><SPAN lang=en-us> <FONT face=Calibri>having the mole</FONT></SPAN><SPAN lang=en-us><FONT face=Calibri>cules fall apart.</FONT></SPAN></P></BLOCKQUOTE><BR>this could be a weight issue (weight between real-space target and restraints). In general I didn't find it too beneficial doing real-space refinement globally, although I've seen cases where it made a good difference (but at higher than 3A resolution). You may try to switch to "simple" target (to make it run much faster) and turn on the weight optimization:<BR><BR> real_space_refinement {<BR> mode = *simple diff_map<BR> target_weights = value *grid_search gradients_ratio<BR> rmsd_max_bonds = 0.05<BR> rmsd_max_angles = 5<BR> grid_search_scales = 0.25 0.5 0.75 1 1.25 1.5 1.75 2 2.5 3<BR> }<BR><BR><BR>"fix_rotamers=true" (local real-space refinement for the residues that really need it, as determined automatically) is much better option. I thoroughly tested it up to 3A resolution and in all test cases it worked just great. Try it and see what happens for your data.<BR><BR>Pavel.<BR><BR><BR><BR></DIV></includetail></DIV>