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 [email protected]

Hi Peter, You could do something along these lines: 1. take the model that you want fixed (perhaps RNA + existing protein model) as "starting.pdb" 2 then run autobuild with phenix.autobuild data=data.mtz seq_file=seq.dat \ input_lig_file_list="starting.pdb" \ helices_strands_only=True \ refine=False where helices_strands_only=true will find the helices (and strands...I don't think you can turn that off right now) only, but not try regular model-building. Alternatively, you can try: phenix.autobuild data=perfect.mtz model=starting.pdb insert_helices=True \ helices_strands_start=False build_outside=False fit_loops=False use_resolve_fragments=False \ connect=False skip_combine_extend=True number_of_parallel_models=1 \ seq_file=seq.dat refine=False rebuild_in_place=False number_of_models=0 \ keep_pdb_atoms=False which will just try to insert helices using phenix.find_helices_strands and density modify, skipping all other build steps. There isn't any way to conveniently use both build_outside_model and helices_strands_only at the moment, however. Let me know if these don't do what you need, All the best, Tom T

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Dear Phenix users,

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 ?

Many thanks in advance for your advice

-- Peter _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb