<div>Hi Sabine,</div>
<div> </div>
<div>I believe the comparison should be with same input, not output of one piped into another.</div>
<div> </div>
<div>How different are the geometry? Different programs use different algorithm and different xray:geometry term by default. Hence, it might only make sense if the RMSD are almost exactly the same. Furthermore, is one program detecting NCS or twining or building waters automatically? Then everything is blown up anyway.</div>
<div> </div>
<div>In any case, refinemt program A vs. B is an interesting topic! I would not start one.. ;)<br></div>
<div>MFG,</div>
<div>Partha<br><br></div>
<div class="gmail_quote">On Fri, Aug 12, 2011 at 5:19 PM, Sabine Schneider <span dir="ltr"><<a href="mailto:sabine.schneider@mytum.de">sabine.schneider@mytum.de</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">Hello,<br><br>I am refining a structure at 2.1A solved by MR. For curiosity I'm testing things like 'shaking' coordinates, simulated annealing, refinement Refmac vs Phenix and so on, to see what influence that has on stats, maps etc.<br>
<br>For instance after MR I did a bit of shaking the coordinates with pdbset (noise 0.1), followed by simulated annealing in Phenix.<br>Phenix states after SA:<br><br>Start R-work = 0.2671, R-free = 0.2992<br>Final R-work = 0.2312, R-free = 0.2666<br>
<br>When I use the output pdb of phenix directly in Refmac (with same mtz as input for Phenix)<br>Refmac tells me:<br>Initial R factor 0.2392 R free 0.2887<br><br>So I am quite puzzled about the discrepancy. Or can someone tell me if I made an error in reasoning somewhere?<br>
<br>Thanks a lot for the help!<br>Sabine<br><br>______________________________<u></u>_________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/<u></u>mailman/listinfo/phenixbb</a><br></blockquote></div><br>