[phenixbb] nucleic acid secondary restraints breaking in 1.7.1-743

Nathaniel Echols nechols at lbl.gov
Mon Aug 15 08:51:02 PDT 2011

On Mon, Aug 15, 2011 at 8:23 AM, Francis E Reyes
<Francis.Reyes at colorado.edu> wrote:
> How unfortunate! Statistical model for missing atoms was dropping my R/Rfree
> about 10% (using 1.7.1-743).

Yeah, it tends to do that. . . although there is some debate about
which R-factors should really be reported, given the difficulty of
reproducing the lower values.  The real benefit to this feature is
improved map quality.

> Is there a nightly that didn't drop use_statistical_model_for_missing_atoms
>  but still has working secondary_structure nucleic acid restraints?

I'm not sure when this broke - in theory there were a couple of weeks
overlap in June, but there may have been other problems with the
missing atoms feature.  Pavel would know for sure.

> I guess the other option is to generate the restraints myself ....

This may be a good intermediate solution:


I had meant to add an option to output the base pair restraints using
the existing custom bond syntax, but haven't had time to do that yet.


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