[phenixbb] High B-factors after Phenix restrained refinement -- peptide building

Tom Terwilliger terwilliger at lanl.gov
Fri Dec 16 07:32:23 PST 2011

Hi Dialing,

You should be able to build the peptide in either of 2 ways:

1. Cut out the density for the peptide with phenix.cut_out_density and build into cutout.mtz with phenix.build_one_model, supplying the sequence of the peptide, and not refining the model. This will just build the peptide. Then you can translate the model that is built back using phenix.cut_out_density.

2. Alternatively, you can put your data file and your map coefficients, and complete sequence file including the peptide into phenix.autobuild and it should try to build the peptide in addition to the rest of your model.  You can also include your working model to speed it up.

All the best,
Tom T

On Dec 16, 2011, at 1:04 AM, Dialing Pretty wrote:

> 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 <nechols at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org> 
> 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 <2dd13 at queensu.ca> 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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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
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ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
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CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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