Hi Nat,
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.
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.
I am looking forward to getting your reply.
Cheers,
Dialing
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From: Nathaniel Echols
I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of rigidbody refinement with Phenix Refine I proceeded to restrained refinement. The R/Rfree from the refinement decreased nicely as expected but the B average is at ~100 (using Group B factor refinement option). I took the same model and mtz through Refmac and the B average is about ~40. Has anyone experienced this before? I am almost positive it maybe a setting issue in Phenix Refine that i should be looking at to get the B factors to refine correctly.
How are you calculating the average B? Refmac prints "residual" B-factors in the B column of ATOM records - these do not include the contribution from TLS and Ucryst (an overall B-factor for the entire crystal). In Phenix, the ATOM records always have the total isotropic B-factor, and this will always be higher than the equivalent in Refmac. So it's quite likely that both programs are correct, they're just reporting very different things. (And for what it's worth, a mean B-factor of 100 is totally normal at 3.3A resolution.) -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb