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

Wai-Ching Hon hon at mrc-lmb.cam.ac.uk
Fri Aug 28 00:35:08 PDT 2009

Dear Sean,

That sounds wonderful. Can I have your scripts too?

many thanks


Sean Johnson wrote:
> Gino,
> 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
>> 233 South 10th Street - Room 826
>> Philadelphia PA 19107
>> Office (215) 503 4573
>> Lab    (215) 503 4595
>> Fax    (215) 923 2117
>> E-mail:   gino.cingolani at jefferson.edu
>> ******************************************************************************
>> "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza"
>> ("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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