[phenixbb] Autobuild at 5A resolution
petgxray at gmail.com
Thu Sep 17 00:23:53 PDT 2009
Thanks. The problem is that it is a big complex with many chains and I think
that giving a sequence to the program will only confuse it. That is why I
wanted to use phenix.find_helices_strand which does not require sequence but
as I understand is not part of Autobuild (am I wrong ?).
On Thu, Sep 17, 2009 at 12:24 AM, Nathaniel Echols <NEchols at lbl.gov> wrote:
> On Sep 16, 2009, at 3:05 PM, Peter Grey wrote:
> > I am trying to solve a big RNA/protein complex at 5A resolution.
> > Phases come from MR solution with a partial model in Phaser. Thanks
> > to NCS the map after density modification in RESOLVE is of
> > reasonable quality for this resolution and new secondary structures,
> > out side of the model, can be detected.
> > I would like to improve the maps and model with something like a
> > poor man's version of AutoBuild. An Autobuild for very low
> > resolutions that does not include refinement but iteratively
> > carries out density modification and identification of helices/
> > strands outside of the model with phenix.find_helices_strand.
> > Does this sound feasible, Are there already scripts the follow such
> > a scheme ?
> Use a command like this:
> phenix.autobuild model.pdb data.mtz seq_file=seq.dat
> rebuild_in_place=False helices_strands_only=True refine=False
> (This is from the most recent documentation - but I think it's the
> same in 1.4-3.)
> I'm not sure whether helices_strands_only works for RNA too, although
> AutoBuild certainly does build RNA.
> Nathaniel Echols
> Lawrence Berkeley Lab
> NEchols at lbl.gov
> phenixbb mailing list
> phenixbb at phenix-online.org
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