<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">I find (for RNA at least ) that 10-100 times less the current value ( I think it's 0.01) for wxc_scale to keep rigid geometry. <div><br></div><div>FR</div><div><br><div><div>On Dec 10, 2009, at 8:38 AM, Pei-Chun Lin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Hi,<span class="Apple-converted-space"> </span><br><br>When talking about "put much more weight on geometry restraints to avoid overfitting", what wxc and wxu value will you suggest to use for a 4A structure?<br>I am working on a 3.5A structure and have no experience of adjusting weight value before. Any suggestion will be very helpful to me.<br><br><br>PC<br><br><br><hr id="stopSpelling">Date: Tue, 8 Dec 2009 20:12:29 -0800<br>From:<span class="Apple-converted-space"> </span><a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a><br>To:<span class="Apple-converted-space"> </span><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>Subject: Re: [phenixbb] refinement<br><br>Hi,<br><br>although I've seen cases like yours when SA in Cartesian space did miracles, in many of cases modeling at 4A resolution is a tough problem.<span class="Apple-converted-space"> </span><br><br>Since clearly SA didn't work out (given R/Rfree ~ 37/50% and the starting 48/50), I would try splitting your model into rigid domains and refine each as a rigid body. Plus, I would refine one isotropic B per residue or per domain (try both). This is a few minutes to try so why don't you do so.<br>Also, I would still combine it (rigid body and B-factor refinement) with Cartesian SA, but I would put much more weight on geometry restraints to avoid overfitting.<br><br>As you probably aware of, in phenix.refine you can run combined refinement jobs, for example, consisting of SA, rigid body, B-factor refinement and so on. So I would recommend playing with the above suggestions to see if it works. Plus,<span class="Apple-converted-space"> </span><b>don't forget looking at the maps - may be you manage to fit something manually.</b><br><br>By the way, which R-factors you get if you run:<br><br>phenix.model_vs_data data.mtz model.pdb<br><br>(phenix.model_vs_data will account for twinning (if any) using Xtriage automatically) ?<br><br>Write us if you have questions.<br><br>Good luck,<br>Pavel.<br><br><br><br>On 12/8/09 7:02 PM, r n wrote:<blockquote cite="mid:234998.1239.qm@web33308.mail.mud.yahoo.com"><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><div><span style="font-family: tahoma, 'new york', times, serif; ">Thanks a lot.<span style="font-family: arial, helvetica, sans-serif; "><span class="Apple-converted-space"> </span>I did download the new -dev249 and did cartesian SA, R goes down to 37 but R-free (50) did not.<span class="Apple-converted-space"> </span></span></span><br>Any suggestions?<br><br><br></div><div style="font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><br><div style="font-family: arial, helvetica, sans-serif; font-size: 13px; "><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold; ">From:</span></b><span class="Apple-converted-space"> </span>Ralf W. Grosse-Kunstleve<span class="Apple-converted-space"> </span><a class="ecxmoz-txt-link-rfc2396E" href="mailto:rwgk@cci.lbl.gov"><rwgk@cci.lbl.gov></a><br><b><span style="font-weight: bold; ">To:</span></b><span class="Apple-converted-space"> </span><a class="ecxmoz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><b><span style="font-weight: bold; ">Sent:</span></b><span class="Apple-converted-space"> </span>Tue, December 8, 2009 3:34:09 PM<br><b><span style="font-weight: bold; ">Subject:</span></b><span class="Apple-converted-space"> </span>Re: [phenixbb] refinement<br></font><br>> I do have very low resolution data (around 4 ang), what are<br>> the efficient way of doing refinement, either rigid body alone or<br>> rigidbody and tls or individual with group_adp. I did both, but not<br>> much significant changes in Rfree stays around 48/50%.<br><br>You could also try Cartesian or torsion-angle simulated annealing.<br>I'd try both. In my experience Cartesian SA often works better even<br>at low resolution.<br>If you get errors running torsion-angle annealing, please try<br>the latest nightly build (dev-249) since I've fixed several<br>problems since the 1.5-2 release.<br><br>> Also I do have other questions<br>> <span class="Apple-converted-space"> </span><br>> 1. While doing rigid body refinement, phenix complaint about the<br>> special position and could not perform rigid body refinement,<br>> whereas individual site refinement is working fine. I do have to<br>> delete the atom in special position for rigid body refinement?<br><br>You could use<br> sites.rigid_body = ...<br>to select the bodies you want to refine. The rest (including your<br>atom on the special position) will not move.<br><br>Ralf<br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><span><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a></span><br></div></div></div><br><pre><hr size="4" width="90%"><br>_______________________________________________<br>phenixbb mailing list<br><a class="ecxmoz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a class="ecxmoz-txt-link-freetext" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br> </pre></blockquote><br><hr>Keep your friends updated�<span class="Apple-converted-space"> </span><a href="http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_5:092010" target="_new">even when you�re not signed in.</a><span class="Apple-converted-space"> </span>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></div></span></blockquote></div><br><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>---------------------------------------------<br>Francis Reyes M.Sc.<br>215 UCB<br>University of Colorado at Boulder<br><br>gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D<br><br>8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D</div></div></span> </div><br></div></body></html>