<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yui_3_16_0_1_1423974666549_16348"><span></span></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1423974666549_16359" dir="ltr">Dear All,</div><div class="qtdSeparateBR" id="yui_3_16_0_1_1423974666549_16359" dir="ltr"><br></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1423974666549_16359" dir="ltr">Then what is rsrg?</div><div class="qtdSeparateBR" id="yui_3_16_0_1_1423974666549_16359" dir="ltr"><br></div><div class="qtdSeparateBR" id="yui_3_16_0_1_1423974666549_16359" dir="ltr">Smith<br><br></div>  <div class="yahoo_quoted" id="yui_3_16_0_1_1423974666549_16384" style="display: block;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;" id="yui_3_16_0_1_1423974666549_16383"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;" id="yui_3_16_0_1_1423974666549_16382"> <div dir="ltr" id="yui_3_16_0_1_1423974666549_17364"> <font size="2" face="Arial" id="yui_3_16_0_1_1423974666549_17363"> On Wednesday, January 21, 2015 12:54 AM, Engin Özkan &lt;eozkan@uchicago.edu&gt; wrote:<br> </font> </div>  <br><br> <div class="y_msg_container" id="yui_3_16_0_1_1423974666549_17027">Just a correction: "adp" is not anisotropic displacement parameters, but <br clear="none">"Atomic Displacement Parameters". ADP is actually the proper name for <br clear="none">B-factors. In phenix.refine, "adp" step can include isotropic ADP <br clear="none">refinement, anisotropic ADP refinement, TLS refinement, or combinations <br clear="none">of those.<br clear="none"><br clear="none">There is also "nhq" or something like that among the steps phenix.refine <br clear="none">performs. It is for flipping sidechains (by 180 degrees) of residues <br clear="none">that are hard to distinguish one way or the other based on clashes and <br clear="none">hydrogen bonding. Obviously, it involves Asn, Gln and His. This step, <br clear="none">while time consuming sometimes, is useful and should be performed, to <br clear="none">prevent yourself from embarrassment by claiming hydrogen bonds with no <br clear="none">donors and two acceptors, for example.<br clear="none"><br clear="none">Engin<br clear="none"><br clear="none">On 1/20/15 4:17 AM, Christian Roth wrote:<br clear="none">&gt; Hi,<br clear="none">&gt;<br clear="none">&gt; bss: bulk solvent scaling<br clear="none">&gt; rsrl: real space rotamer refinement? Did you select rotamer correction <br clear="none">&gt; or realspace refinement in your strategy?<br clear="none">&gt; adp: ainsotropic displacement parameters means simple B-Factor refinement<br clear="none">&gt;<br clear="none">&gt; Cheers<br clear="none">&gt;<br clear="none">&gt; Christian<br clear="none">&gt;<br clear="none">&gt; Am 20.01.2015 um 01:49 schrieb Smith Lee:<br clear="none">&gt;&gt; Dear All.<br clear="none">&gt;&gt;<br clear="none">&gt;&gt; In the Phenix refine "run status" window, with the progression of the<br clear="none">&gt;&gt; refinement, it occurs 3' bss, 3' rsrl, 3' xyz, 3' adp (for 3rd round of<br clear="none">&gt;&gt; refinement). I guess xyz means the strategy is for x, y, z coordinates?<br clear="none">&gt;&gt; Then what do bss, rsrl and adp mean?<br clear="none">&gt;&gt;<br clear="none">&gt;&gt; I am looking forward to getting your reply.<br clear="none">&gt;&gt;<br clear="none">&gt;&gt; Smith<br clear="none">&gt;&gt;<br clear="none">&gt;&gt;<br clear="none">&gt;&gt; _______________________________________________<br clear="none">&gt;&gt; phenixbb mailing list<br clear="none">&gt;&gt; <a shape="rect" ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br clear="none">&gt;&gt; <a shape="rect" href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><div class="yqt3106090101" id="yqtfd26080"><br clear="none">&gt;&gt;<br clear="none">&gt;<br clear="none">&gt;<br clear="none">&gt; _______________________________________________<br clear="none">&gt; phenixbb mailing list<br clear="none">&gt; <a shape="rect" ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br clear="none">&gt; <a shape="rect" href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br clear="none"><br clear="none">_______________________________________________<br clear="none">phenixbb mailing list<br clear="none"><a shape="rect" ymailto="mailto:phenixbb@phenix-online.org" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br clear="none"><a shape="rect" href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br clear="none"></div><br><br></div>  </div> </div>  </div> </div></body></html>