[phenixbb] ncs - PS
Pavel Afonine
PAfonine at lbl.gov
Tue May 5 14:38:37 PDT 2009
This might be good to mention:
> Remove all waters, reset all B-factors to average one, shake
> coordinates to achieve rmsd~1A and then run 10-20 macro-cycles of
> refinement in phenix.refine (or until the R-factors stop changing),
you can perform all these manipulations using phenix.pdbtools.
Example:
phenix.pdbtools model.pdb remove="water"
or equivalently:
phenix.pdbtools model.pdb keep="not water"
phenix.pdbtools model.pdb set_b_iso=25
phenix.pdbtools model.pdb sites.shake=0.75
For more examples and general information see phenix.pdbtools manual:
http://phenix-online.org/documentation/pdbtools.htm
Pavel.
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