[phenixbb] sequence independent model building possible?

[Paul Adams]

You could try a couple of things:

- running phenix.structure_search (from the command line only at the moment) on your current model
- running autobuild without rebuild in place

> On Feb 4, 2016, at 10:01 PM, Kaushik Hatti <hskaushik at gmail.com> wrote:
> 
> Hello,
> 
> Is abinitio model building possible for a map with poly alanine model at 1.9A resolution?
> 
> We thought we had crystallised our protein of interest X, collected data at 1.9 A and all attempts to solve protein X (which has many homologs) through MR failed.  All attempts to re-crystallise the same protein also failed. 
> 
> Now, we think the initial protein which got crystallised could be a contaminant (we don't have any crystals left from this batch to check for the sequence of the crystallised protein).  Through various methods (and a bit of luck) we have arrived at a decent map with LLG : 3600 and TFZ: 22 and R/Rfree : 37/41 (for a poly alanine model).
> 
> I believe these scores indicate right fold.  As I still don't know the sequence information, is it possible to build sidechains directly from the map (I could only identify a couple of residues and the model largely remains PolyAla)?  Autobuild with Rebuild-in-place didn't help in identifying any more residues.
> 
> I have also searched PDB database for similar structures. But, none of those are either from our expression system (E. coli) or organism of our protein of interest. Neither did I find any similar sequences from E. coli or our organism of interest.
> 
> Any leads/suggestions would be helpful.
> Thanks, 
> Kaushik,
> MRN Murthy lab,
> MBU,
> IISc, India
> 
> -- 
> Stupidity is everyone’s birthright.  However, only the learned exercise it!
> --Kaushik (28Oct2014)
> 
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Paul Adams
Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

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