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

Gino Cingolani Gino.Cingolani at jefferson.edu
Tue Aug 25 17:01:33 PDT 2009

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 Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
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E-mail:   gino.cingolani at jefferson.edu
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("You were not born to live like brutes, but to follow virtue and knowledge")
Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120) 

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