PAfonine at lbl.gov
Fri Sep 11 08:28:06 PDT 2009
> If I use the simple command phenix.refine data.mtz model.pdb
> what strategy is used by default?
quoting phenix.refine manual:
"phenix.refine data.hkl model.pdb
This will perform coordinate refinement and restrained ADP refinement.
Three macrocycles will be executed, each consisting of bulk solvent
correction, anisotropic scaling of the data, coordinate refinement (25
iterations of the LBFGS minimizer) and ADP refinement (25 iterations of
the LBFGS minimizer). At the end the updated coordinates, maps, map
coefficients, and statistics are written to files. "
One more remark: if your input ADPs are anisotropic, then they will
refined as individual anisotropic (if resolution is high enough), if
they are isotropic, then they will be refined as isotropic.
> When do I need to specify strategy?
You need to use it when you need to change the default protocol in order
to fit better your particular situation. For example: if you need to
inclcude TLS or rigid-body refinement, if resolution is low enough and
you need to switch from refinement of individual isotropic ADPs to group
B, etc - the list is long.
> When is TLS beneficial?
Always. See slides #30-#36 here:
> I have 90% of residues with very good density,
> but about 10% (C-terminal helix+ loop) with very poor density. What
> would be the best strategy for the poor region?
It's hard to say without specifically looking at it...
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