[phenixbb] Autobuild at 5A resolution

Nathaniel Echols NEchols at lbl.gov
Wed Sep 16 15:24:03 PDT 2009

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

More information about the phenixbb mailing list