[phenixbb] phenix.refine questions: weights, docs, etc.

Frank von Delft frank.vondelft at sgc.ox.ac.uk
Tue May 29 07:22:16 PDT 2007

Hi, four questions on phenix.refine:

1) What's the reason for refining bss, xyz and adp in separate cycles?  CNS
does that too while refmac (I believe) refines them simultaneously.  I
suspect I missed something, but I thought the power of ML refinement is that
no refinable parameters are held constant if they're not supposed to be.
(At least, wasn't that the big deal in Sharp when it came out?)

2) How does one figure the right restraint weights?  (wxc and wxc).  In
refmac, I've always calibrated the weight with rmsd(bonds), tightening it
until rmsd(bonds) is ~0.018 (or below for lower reso);  invariably this is
where Rfree will decrease furthest and smoothly as well (i.e. without that
silly rise at the end.)

With phenix.refine I'm finding that I only get Rfree to drop monotonously
when I tighten the weights (both wxc and wxu) so much that rmsd(bonds) goes
down to ~0.002.  Would there be a different way to do this?

3) There isn't currently torsional refinement, is there?  For
high-temperature simulated annealing, I mean.  I'm having the same
weight-adjustment question for SA, except is harder to fiddle with because
jobs take so long, but with torsional that becomes moot.  Or should one
always put very tight weights on for SA?

4) Is there good documentation for all the loads and loads of keywords?  The
names themselves are just descriptive enough to be interesting, but
obviously not enough to be informative if I don't just want the black box.

Nice program, though, got to say...

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