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Re: [ccp4bb]: dodgy indexing



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The mosaicity parameter in denzo can be compared to the Lemon-Larson
peak integration limits for (small molecule) diffractometer scans.  The
main volume of the peak is integrated and the 'tails' (in phi rotation
for oscillation photos) are excluded.  The mosaicity chosen by
denzo/scalepack generally results in the best I/s for the  reflection,
with only a fraction (<1% ?)  of the total integrated intensity going to
the tails.  This is not generally noticeable, except at low resolution
where the 'tails' have sufficient intensity to be observable in the
oscillation photo.  Other reasons for observing unindexed reflections at
low resolution include TDS (thermal diffuse scattering).  Increasing the
denzo/scalepack mosaicity parameter a 'little bit' is I believe a common
practice, and should not severely affect the data quality (I/s).  While
using incorrect error models (in scalepack) is probably a more harmful
and common practice to avoid.


Lauris Kemp wrote:

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>
> Hello
> I'm trying to index a data set with denzo. The problem is with
> mosaicity-it looks about 1 but at this value it misses out some low
> resolution spots and seems to overfit for the number of spots at high
> resolution. Thought it might be misindexed but did a direct beam shot
> and the beam values look about right. It manages to autoindex it fine
> and the chi values are also fine.
> Lauris

--

Best Regards,

Mark

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Mark A. White, Ph.D.                                    Tel:
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