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

From: Nathaniel Echols <[email protected]>
To: PHENIX user mailing list <[email protected]>
Sent: Friday, 16 December 2011 3:31 PM
Subject: Re: [phenixbb] High B-factors after Phenix restrained refinement

On Thu, Dec 15, 2011 at 2:20 PM, Da Duan <[email protected]> wrote:
> 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
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