<div>Hi </div>
<div> </div>
<div>i want to make one clarification here that clashes appear when i used the mtz file generated by CCP4 along with the MR solution from Phaser in Refmac 5. Refinemnet is fine in Phenix with R and Rfree of 25/30.<br>i am using Phenix 1.7.1.743. <br>
</div>
<div class="gmail_quote">On Tue, Dec 13, 2011 at 1:38 PM, Nathaniel Echols <span dir="ltr"><<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div class="im">On Mon, Dec 12, 2011 at 8:26 PM, intekhab alam <<a href="mailto:faisaldbg@gmail.com">faisaldbg@gmail.com</a>> wrote:<br>> I have a 3.0A dataset of a protein-protein complex. I used one of the<br>
> protein structure solved previously as a template and used phaser in CCP4 as<br>> well as in phenix. I used the sca file in phenix which gave a solution with<br>> 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the<br>
> converted .mtz file which gave 6 molecules in ASU but with a different<br>> packing. In both the cases map fits well in the model and there is some<br>> extra density that may correspond to second protein partner of the complex<br>
> molecule. when i tried to use the MR solution generated in phenix with the<br>> mtz file from ccp4 the model shows a lot of clashes.<br><br></div>The two solutions are probably equivalent under crystallographic<br>
symmetry - they simply represent different versions of the ASU. It's<br>possible that they also have different origins, but I can't tell from<br>your description whether this is the case. What kind of refinement<br>
are you running that results in clashes, and what is the clashscore<br>for the resulting model? (Please include the program version.) As a<br>general rule, reciprocal-space refinement without phases should work<br>regardless of the origin or ASU, so it could just be a weighting<br>
problem. If you are running real-space refinement that is potentially<br>more problematic, but I doubt that's the problem in this case.<br><br>-Nat<br>_______________________________________________<br>phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote>
</div><br><br clear="all"><br>-- <br>INTEKHAB ALAM<br>LABORATORY OF STRUCTURAL BIOINFORMATICS<br>KOREA UNIVERSITY, SEOUL<br>