<div dir="ltr">On Thu, Oct 2, 2014 at 7:34 AM, Sneha Rangarajan <span dir="ltr"><<a href="mailto:rsneha@umd.edu" target="_blank">rsneha@umd.edu</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">1) When is a good time to start building the peptide into the density (should I wait until Rfactors improve significantly)?<br></blockquote><div><br></div><div>I would advise waiting until the rest of the model is as good as possible. That way you can use the difference map as a paper figure without needing to do any extra refinement to remove model bias later.</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
2) If so, should I be masking the peptide density somehow so that further refinement doesn't flatten out that density?<br></blockquote><div><br></div><div>Further refinement is probably going to make the density clearer, if it's at full (or near-full) occupancy.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
3) What is a general good strategy for lowering Rfactors? (Esp if the gap between Rwork and Rfree is high..like 28/40 or so)?<br></blockquote><div><br></div><div>Several things to try:</div><div>- much longer refinement, say 10 macro-cycles instead of 3 (and even more may be helpful)</div><div>- simulated annealing - although this sometimes has a tendency to overfit, but right now that's not as big a problem</div><div>- weight optimization will reduce the gap between R-free and R-work, although it will also slow down convergence</div><div><br></div><div>But you should also try to make the model as complete as possible - AutoBuild usually leaves out some residues, and rebuilding them should reduce your R-factors by quite a bit. You may be able to simply copy over appropriate pieces of the original model if they fit the map well (or can be adjusted easily).</div><div><br></div><div>-Nat</div></div></div></div>