<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="RIGHT: auto"><SPAN style="RIGHT: auto">Dear All and <VAR id=yui-ie-cursor></VAR>Nat,</SPAN></div>
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<div style="RIGHT: auto"><SPAN style="RIGHT: auto">The Ming webpage is following, which I am also in the learning process.</SPAN></div>
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<div style="RIGHT: auto"><A style="RIGHT: auto" href="http://kinemage.biochem.duke.edu/teaching/workshop/MolProbity/" target=_blank><FONT style="RIGHT: auto" color=#234786>http://kinemage.biochem.duke.edu/teaching/workshop/MolProbity/</FONT></A></div>
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<div style="RIGHT: auto">Will you please also introduce me a webpage based on which I can reduce my rotamer outlier (currently 8% by Phenix evaluation).</div>
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<div style="RIGHT: auto">In addition here I have a basic concept which I am confused:</div>
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<div style="RIGHT: auto">The outlier here (for rotamer) analyzed by Phenix evalutation is defined by that the outlier rotamer conformaton does not comply with the statstics of the rotamer conformation of that residue in the published PDB, or it is because the so-called rotamer outlier is caused by its the outlier rotamer conformation<VAR id=yiv1773066337yui-ie-cursor></VAR> does not comply with the electronic density map?</div>
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<div style="RIGHT: auto">I am looking forward to getting a reply from you.</div>
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<div style="RIGHT: auto">Cheers,</div>
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<div style="RIGHT: auto">Dialing</div>
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<DIV style="BORDER-BOTTOM: #ccc 1px solid; BORDER-LEFT: #ccc 1px solid; PADDING-BOTTOM: 0px; LINE-HEIGHT: 0; MARGIN: 5px 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; HEIGHT: 0px; FONT-SIZE: 0px; BORDER-TOP: #ccc 1px solid; BORDER-RIGHT: #ccc 1px solid; PADDING-TOP: 0px" class=hr contentEditable=false readonly="true"></DIV><B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Nathaniel Echols <nechols@lbl.gov><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> PHENIX user mailing list <phenixbb@phenix-online.org> <BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Sunday, 4 December 2011 4:56 AM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> Re: [phenixbb] the Ming dial<BR></FONT><BR>On Sat, Dec 3, 2011 at 3:00 AM, Dialing Pretty <<A href="mailto:hdc123hdc123@yahoo.com" ymailto="mailto:hdc123hdc123@yahoo.com">hdc123hdc123@yahoo.com</A>> wrote:<BR>> In the Ming dial, there is a occupancy (%), which indication of excellent
,<BR>> good, etc. Does it mean if I choose the "occupancy" of excellent, the<BR>> rotamer outlier ratio will be lowered? My crystal has a resolution of 2.8,<BR>> and I find no matter how I turn the dial, the original fits the map best.<BR>> Currently my rotamer outlier is 8%, thus I need the way to have it solved.<BR><BR>I'm not familiar with the program Ming - can you point us to a web page?<BR><BR>Regarding rotamer outliers, it may be difficult to completely<BR>eliminate them at this resolution - the dihedral angle restraints are<BR>not very tight. However, you may need to adjust the backbone to get a<BR>rotameric sidechain conformation to fit the density properly (before<BR>and after refinement).<BR><BR>-Nat<BR>_______________________________________________<BR>phenixbb mailing list<BR><A href="mailto:phenixbb@phenix-online.org" ymailto="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><BR></DIV></DIV></div></body></html>