On Tue, Nov 13, 2012 at 5:33 PM, Qiang Chen <span dir="ltr"><<a href="mailto:chen@red.dfci.harvard.edu" target="_blank">chen@red.dfci.harvard.edu</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I have a 3.05Å structure. I refine it to Rwork=25.2 Rfree=28.81. I use<br>
Molprobity to check the structure. The clash score is 100th and Molprobity<br>
score is 99th. I was suggested to run simulated anneal to help reduce<br>
Rwork and Rfree. I tried Cartesian and Torsion and different seed. The<br>
best result I got is: torsion anneal, start_temp=2500,final_temp=300,<br>
random_seed=4250146. The Rwork:25.8, Rfree=31.2. I checked the new model<br>
and found that some places in a domain were not correctly traced. The<br>
density for that domain is not good and have several flexible loops. My<br>
question is: does simulated anneal always work and reduce Rwork/Rfree?</blockquote><div><br></div><div>No, especially when the structure is nearly finished.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
At the final stage of refinement, does it necessary to use simulated anneal<br>
again?<br></blockquote><div><br></div><div>Definitely not necessary. Simulated annealing is a good way to improve a model that fits the data poorly, or to remove model bias, but at the end of refinement you should be much more conservative.</div>
<div><br></div><div>There are several other potential ways to reduce the R-free - such as using TLS, or optimizing the weights. But you already have excellent geometry and your R-free and R-free/R-work gap are both reasonable for that resolution, so it's possible that further refinement won't help.</div>
<div><br></div><div>-Nat</div></div>