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 ?).

Peter.


On Thu, Sep 17, 2009 at 12:24 AM, Nathaniel Echols <NEchols@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
510-486-5136
NEchols@lbl.gov



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--
Peter