5 May
2009
5 May
'09
9:38 p.m.
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.