Is this map a total OMIT map like SFCHECK does or a SA-OMIT map like CNS does? Jianghai On Dec 29, 2006, at 12:53 PM, Thomas C. Terwilliger wrote:
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
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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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