[phenixbb] sequence independent model building possible?

Paul Adams pdadams at lbl.gov
Fri Feb 5 11:48:23 PST 2016

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
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