On Tue, Nov 15, 2011 at 7:27 AM, Yarrow Madrona
One more question. When you refine in subsequent rounds I read that phenix.refine will refine as anisotropic because of the ANISOU labels attached to the PDB. Is it necessary to enter something like "stragegy=tls+isotropic"? I am just worried that if I explicitly ask for individual isotropic refinement this might occur without tls refinement.
This is only a problem at relatively high resolution - the key parameter is switch_to_isotropic_high_res_limit = 1.5 .type = float .help = If the resolution is lower than this limit, all atoms selected \ for individual ADP refinement and not participating in TLS \ groups will be automatically converted to isotropic, whether or \ not ANISOU records are present in the input PDB file. .short_caption = Resolution limit for automatic anisotropic ADPs (".short_caption" is what appears in the GUI) So if your resolution is worse than 1.5, I think it will do what you want automatically. Otherwise, you can avoid the problem by converting your PDB file to isotropic atoms (convert_to_isotropic=True, I think - phenix.pdbtools can also do this), and/or specify refine.adp.isotropic="not (element H or element D)". -Nat