[buster-discuss] rejected refleXions in refine version 2.10.2
vonrhein at globalphasing.com
Fri Apr 21 11:56:13 CEST 2017
(sorry for the late reply).
On Thu, Apr 06, 2017 at 04:29:15PM -0400, wtempel wrote:
> 01-BUSTER/Cycle-5/LIST.html includes a dead link to a file
Correct: we remove a fair amount of files that are not really if
interest to users (and even we developers hardly ever miss them unless
we do some hard-core, open-heart surgery on BUSTER).
> Is there another file that would allow me to view an analysis of
> rejected reflexions?
The above file (hkl_reject.html) does not contain rejected reflections
in the sense that you are thinking about: it lists reflections that
are rejected from refinement because their test-set flag marks them as
being in the "free" set.
> In my case, the lower resolution limit changes from 25 Å (hklin) to
> 12 Å (reported in refine.pdb), corresponding to approx. 25
This is done automatically based on some very (!) poor correlations at
low resolution in the reciprocal space correlation plots. You could
switch off that behaviour using
However, it nearly always points to some problems in processing (beam
stop masking etc) or collection (overloads etc).
> The diffraction images may have had some overloaded pixels, and
> scaling statistics show the low resolution shell less complete than
> the overall data set.
That might be the explanation: you now have only (relatively) weak
reflections in the low-resolution range and all strong reflections
required to model the bulk solvent contribution reliably are missing
(resulting in poor low-resolution CCs).
> I would like to confirm that those lowest 25 or so reflexions were
> in fact rejected by buster.
Since BUSTER doesn't reject data based on individual reflections, you
can just look at the data in the range 25-12A, i.e.
echo "RESO 999.9 12.0" | mtzutils hklin your.mtz hklout lowres.mtz
mtzdmp lowres.mtz -n -1
> Would the ensuing loss to the quality of my model justify the added
> complexity introduced by possibly merging the high resolution
> (synchrotron) data with an earlier, lower resolution rotating anode
> data set from the same crystal?
Difficult to tell: if you are working on a structure that relies
heavily on good low-resolution data (only low-resolution data
available, disorder, missing domains etc) you will probably see an
effect. The question is if using systematically skewed data at
low-resolution (only weak reflections) is better/worse than not using
the low-resolution data at all.
Trying to combine a high-resolution and low-resolution dataset can be a
tricky business in itself. Doing this for data from different crystals
makes it even more complicated ... and data from different
detectors/instruments will not make it easier.
What is still unclear, missing or disordered in your current model
after BUSTER refinement using data with a low-resolution cutoff of
And what is the high-resolution limit of your data?
Clemens (for buster-develop)
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