[phenixbb] Tracing and refining b-strands at 3.3A resolution

Sean Johnson sean.johnson at usu.edu
Thu Aug 27 14:53:18 PDT 2009


My lab recently refined a 3.4 A structure and dealt with similar 
problems. We found that using secondary structure restraints was the 
only effective way to maintain reasonable geometry during refinement. It 
is kind of a daunting task to input all of the definitions by hand, so 
we wrote a couple python scripts that are integrated with PyMol to write 
the appropriate restraint definition files. All you have to do is click 
on the atoms that you want restrained. You are welcome to the scripts if 
you like. Feel free to contact me if you are interested.

Sean Johnson

Gino Cingolani wrote:
> Hi Phenix community, 
> I'm tracing a 3.3A averaged electron density map of 
> a large macromolecular complex (~18,500 residues in the asymmetric unit). The map has great continuity and appears quite 'tubular'. While it is easy to interpret in a-helical regions, b-strands are more challenging, as I can't see the 'bump' corresponding to the carbonyl. If I built b-strands into the tubular density, refinement usually 'undoes' them and turns them into pseudo-loops/turns. On the positive side, a related molecule (~70% identical to mine) was solved to 1.9A resolution. So my question is, is there a way in Phenix to use a 'reference model' during refinement to force a given stretch of polypeptide chain to 'stay' b-stranded during refinement?
> Thanks in advance for the feedback,
> Gino
> ******************************************************************************
> Gino Cingolani, Ph.D.
> Associate Professor
> Thomas Jefferson University
> Dept. of Biochemistry & Molecular Biology
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Sean Johnson, PhD
R. Gaurth Hansen Assistant Professor
Utah State University
Department of Chemistry and Biochemistry
0300 Old Main Hill
Logan, UT 84322-0300
(435) 797-2089
(435) 797-3390 (fax)
sean.johnson at usu.edu

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