[phenixbb] Weight optimization

Nathaniel Echols nechols at lbl.gov
Wed May 26 08:40:48 PDT 2010

On Wed, May 26, 2010 at 8:30 AM, Pavel Afonine <PAfonine at lbl.gov> wrote:

> Well, I guess better to have it resolution dependent, and best to have it
> local per bond or so. I have no intention to open another can of worms, but
> where those 0.02 and 2 come from? Can you really see that level of details
> at say 2.5A resolution and lower? I guess at that resolutions they should be
> both zero. In contrast, at higher resolution larger deviations are justified
> just by the data and so larger margins in restraints should be allowed. I
> know there is a heap of good papers on this matter, including the recent
> ones, and there are long threads on bb, but to me this question is still
> somewhat open. May be someone on the board can thoroughly/convincingly
> comment on this, summarizing all previous discussions?

My guess would be that the limits are derived from Engh & Huber.  I was
taught to use 0.016 and 1.6; 0.02 and 2 are a bit on the high end but for
very high-resolution structures this wouldn't be inappropriate, and it's
arguably helpful earlier in refinement to let the geometry be a bit looser.
 I don't think it's practical to force them to be zero at high resolution -
it will make it much harder to converge during refinement.  Regardless of
what the limits *should* be at different resolutions, reviewers will expect
something below 0.02/2, and the overwhelming majority of protein structures
will be done at resolutions where these values are indeed appropriate at
upper limits.

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