On Thu, Feb 16, 2012 at 2:51 PM, Wei Shi <span dir="ltr">&lt;<a href="mailto:wei.shi118@gmail.com">wei.shi118@gmail.com</a>&gt;</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&#39;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&#39;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&#39;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>