On Fri, Jun 10, 2011 at 5:43 PM, Jennifer Weinreich <span dir="ltr"><<a href="mailto:jenn.a.weinreich@gmail.com">jenn.a.weinreich@gmail.com</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;">
2) What is the expected (or 'acceptable') gap between R and Rfree at this resolution. (Current R = 27%, Rfree = 33%) Does this sound reasonable?<br></blockquote><div><br></div><div>It's not unreasonable, but you can probably narrow the gap if you get the reference model restraints working. (For comparison, I've spent most of the last week playing around with low-resolution data, and two of my test cases are a 3.6A structure with R/R-free = 0.285/0.335, and a 4.0A structure at 0.27/0.34 - both published, and originally refined with Phenix.)</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">3) It has been suggested to me that I should try adding riding hydrogens during the last round of refinement (to help with geometry). Is this something I should do?<br>
And if so, should I remove them when I deposit the file to the PDB. (Hydrogens at 4.5A are probably going to raise a lot of eyebrows...<br></blockquote><div><br></div><div>It's worth a try, but in my experience this often just makes it worse.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">5) I have been using secondary structure restraints during the refinement, which seems to work reasonably well. I also tried refinement using reference model (the structure of the individual components). But refining with reference models seems to result in high RMSD bonds/angles. Is there something I'm missing?<br>
</blockquote><div><br></div><div>For some reason the reference model restraints often have a weird effect on the automatic weighting. Try optimizing the x-ray/stereochemistry weighting with relatively strict limits for RMS(bonds)/RMS(angles) - on the command line, for instance:</div>
<div><br></div><div>optimize_wxc=True</div><div>bonds_rmsd_max=0.01</div><div>angles_rmsd_max=1.5</div><div><br></div><div>(and in the GUI, it's in the middle of the second tab in the configuration section.)</div><div>
<br></div><div>-Nat</div></div>