Re: [ccp4bb]: Enforcing a sigma(f) cutoff?

[Ethan Merritt <merritt@u.washington.edu>]

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<Flame-retardant ON>

On Friday 31 January 2003 16:09, Mark DePristo wrote:
> For the life in me I cannot figure out how to enforce a sigma(f)
> cutoff in refmac5.  

Don't do that.

> Regardless, I am suspicious that this cutoff accounts for the
> slightly higher R and R-Free values (~ 2%) of my new structure.  Is
> this a reasonable interpretation?  

Yes, but low R factors aren't everything.   You could always just
keep throwing out data until your R factor looked good, but this is
not a statistically justifiable thing to do.

> If so, how can I enforce a sigma(f) data cutoff?

The use of sigma(F) cutoffs in macromolecular work is a hold-over from
the bad old days when (A) data processing procedures did not yield
valid sigmas and (B) refinement programs did not properly use the sigmas
for weighting anyhow.  Those days are hopefully way behind us now, and
you should not reject individual reflections based on sigma(F).

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Truncating to a given resolution based on average F/sigma(F) in the
highest shell is a separate question, and a separate discussion.

-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX:   (206)685-7002