How to handle b-factors at low resolution and very incomplete model?

From: Francis E Reyes
Date: 23 August 2011 18:30


Hi all

What's a way to determining a B-factor to set for all residues of a model at low resolution (4A)? How valid is the wilson B at this resolution? (better than nothing?)

I'm in the process of fitting whole domains into some rasty experimental density maps and was thinking of doing a rigid body or very restrained  ( secondary structure | reference structure | etc ) refinement of the coordinates for helping the fit.

Thanks!

F



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Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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From: Ed Pozharski
Date: 23 August 2011 18:43



Why not refine the overall B-factor?  Even at 4A it should still be
legitimate.

--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
                                               Julian, King of Lemurs

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From: Engin Özkan
Date: 23 August 2011 19:15



I distinctly remember reading a paper where B factors were predicted based on the location of the atoms (core vs exposed, main chain vs side chain) and the predicted values were not that far off. I wonder if B factors could actually be restrained at low resolution towards values reasonable/expected/similar to model values, just as how we put in model restraints for coordinate refinement these days, since many of us working at low resolution have at some point or another experienced catastrophe with B factor refinement. I wonder if this has been tested...

Engin

--
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111

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From: Ethan Merritt
Date: 23 August 2011 20:03



I believe that's called "TLS refinement" :-) :-) :-)

       Ethan
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

On 11:15 Tue 23 Aug     , Engin Özkan wrote:

> I distinctly remember reading a paper where B factors were predicted

> based on the location of the atoms (core vs exposed, main chain vs

> side chain) and the predicted values were not that far off.

Here's one along those lines:

Flexibility and packing in proteins

Bertil Halle

PNAS (2002) 99: 1274 –1279

--

Thanks,

Donnie

Donald S. Berkholz, Ph.D.

Research Fellow

James R. Thompson lab, Physiology & Biomedical Engineering

Grazia Isaya lab, Pediatric & Adolescent Medicine

Mayo Clinic

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