<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Nat,</span></div><div><br><span></span></div><div><span>I have a protein-peptide complex crystal, and I got the 3-D structure of the protein part in the complex by rigid body refinement with isomophous crystal crystal structure as the search model, and I got the peptide structure by Coot peptide building, then I refine the whole protein-peptide complex.</span></div><div><br><span></span></div><div><span>Will you please tell me which Phenix program can be used to build the peptide as I mentioned in the situation above? I want to get a Coot alternative for the peptide building.</span></div><div><br><span></span></div><div><span>I am looking forward to getting your
reply.</span></div><div><br><span></span></div><div><span>Cheers,</span></div><div><br><span></span></div><div><span>Dialing<br></span></div><div><span> </span></div><div><br></div> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight: bold;">From:</span></b> Nathaniel Echols <nechols@lbl.gov><br> <b><span style="font-weight: bold;">To:</span></b> PHENIX user mailing list <phenixbb@phenix-online.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Friday, 16 December 2011 3:31 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [phenixbb] High B-factors after Phenix restrained refinement<br> </font> <br>On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <<a ymailto="mailto:2dd13@queensu.ca"
href="mailto:2dd13@queensu.ca">2dd13@queensu.ca</a>> wrote:<br>> I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of<br>> rigidbody refinement with Phenix Refine I proceeded to restrained<br>> refinement. The R/Rfree from the refinement decreased nicely as expected but<br>> the B average is at ~100 (using Group B factor refinement option). I took<br>> the same model and mtz through Refmac and the B average is about ~40. Has<br>> anyone experienced this before? I am almost positive it maybe a setting<br>> issue in Phenix Refine that i should be looking at to get the B factors to<br>> refine correctly.<br><br>How are you calculating the average B? Refmac prints "residual"<br>B-factors in the B column of ATOM records - these do not include the<br>contribution from TLS and Ucryst (an overall B-factor for the entire<br>crystal). In Phenix, the ATOM records always have the total isotropic<br>B-factor,
and this will always be higher than the equivalent in<br>Refmac. So it's quite likely that both programs are correct, they're<br>just reporting very different things. (And for what it's worth, a<br>mean B-factor of 100 is totally normal at 3.3A resolution.)<br><br>-Nat<br>_______________________________________________<br>phenixbb mailing list<br><a ymailto="mailto:phenixbb@phenix-online.org" 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><br><br> </div> </div> </div></body></html>