[phenixbb] full omit maps

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Dec 29 09:53:05 PST 2006

Hi Miguel,

I'm sorry to have given incorrect instructions!  Here is a corrected
version of how to make a composite omit map with no rebuilding or
refinement in phenix (I just did this to be sure).

If you use a script, add the following lines to your rebuild script:

 rebuild_in_place True       # rebuild existing model...
 rebuild_res_start_list 0    # rebuild only residues 0 to -1 (i.e., nothing)
 rebuild_res_end_list -1
 refine False                # don't refine input model
 n_cycle_rebuild_min 1       # just do one cycle
 n_cycle_rebuild_max 1

If you run from a GUI (I didn't test this, but it should work), set the
same parameters above to these values and it should give you the omit map.

If you just get the overall_best.pdb_OMIT_REGION_1 files then it isn't
working...if you also get overall_best.mtz_OMIT_REGION_1 then it is.  The
final map should be resolve_composite_map.mtz. It is produced after all
the omit region maps are made

Let me know if this doesn't solve the problem!
All the best,

-Tom T

> Hash: SHA1
> Hello everyone,
> I'm trying to obtain a full omit map as it was described by Tom
> Terwilliger in a previous post:
> http://www.phenix-online.org/pipermail/phenixbb/2006-October/000108.html
> However, when I run the AutoBuild strategy asking for no rebuilding / no
> refinement all I get in the FULL_OMIT directory is a collection of pdb
> files named 'overall_best.pdb_OMIT_REGION_x' where 'x' correspond to
> each of the 'omit regions'. But I get no 'resolve_composite_map.mtz'
> whatsoever.
> Surely I'm missing something. I would appreciate your guidance.
> Have all of you an excellent year 2007!
> All the best,
> Miguel
> - --
> Miguel Ortiz Lombardía
> Centro de Investigaciones Oncológicas
> C/ Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> Tel. +34 912 246 900

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