[phenixbb] ncs - PS

[Pavel Afonine]

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.