On Thu, Feb 16, 2012 at 2:51 PM, Wei Shi <span dir="ltr"><<a href="mailto:wei.shi118@gmail.com">wei.shi118@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">
<p class="MsoNormal">I processed the data with XDS in space group P31, and used
*.cns.hkl file from XDSCONV as an input for AutoSol and also include
the sequence for protein only. <span> </span>The
protein dimer has 418 residues and DNA is 32bp. I run Autosol with the default
setting. Below is statistics I got. It seems that I didn’t get anything
promising. Any comment or suggestion about what to try next? Thank you so much!</p>
<p class="MsoNormal">Statistics:<span> </span></p>
<p class="MsoNormal">Top solution: 2<span> </span>Sites:
11.<span>
</span>Space group: P32.<span> </span>FOM:
0.550.<span> </span></p>
<p class="MsoNormal">BAYES-CC: 8.10.<span> </span>Residues:
465<span>
</span>Side-chains: 0.<span> </span><span> </span>Chains:
60. </p>
<p class="MsoNormal">Model CC:<span>
</span>0.67<span>
</span>R-work: 0.4100<span> </span><span> </span>R-free: 0.4569.</p></blockquote><div><br></div><div>At this resolution it's hard to know how much to trust those R-factors, and 60 chains is worrisome, but did you try running MR on the native dataset with the final model yet? It may be too chopped up to be useful in a different crystal form, but if this works you're nearly there.</div>
<div><br></div><div>Other things to try:</div><div>1. Nucleic acids are much easier to see than protein at low resolution - see if you can find the double helix in the density-modified map. (It will probably have protein residues built into it, but hopefully the shape is still distinctive.)</div>
<div>2. Generate an anomalous difference map in phenix.maps using the output model and either the peak or high remote (if you have it) wavelength (you might first need to combine the R-free flags generated by AutoSol with the original anomalous data) and look for clear Se peaks around the heavy atom sites. Also check that the Se sites look like they're plausibly attached to Met residues.</div>
<div>3. Run phenix.find_helices_strands with the final map, and see how that works for MR on the native data.</div><div><br></div><div>-Nat</div></div>