I was very surprised recently when a run of pointless chose to
transform my data into spacegroup I2 [*]. Here are excerpts from the
output log:
%%%%%%%%%%%%
Selecting space group I 1 2 1 as there is a single space group with the
highest score
Space group confidence (= Sqrt(Score * (Score - NextBestScore))) = 0.37
%%%%%%%%%%%%
The input crystal system is C-centred monoclinic
(Cell: 291.8 98.38 148.6 90 120.3 90)
The crystal system chosen for output is body-centred monoclinic
(Cell: 148.6 98.38 252 90 90.33 90)
%%%%%%%%%%%%
Notice that the log file output doesn't say, for instance,
"you might want to consider the non-standard setting I2".
It says "there is a single space group with the highest score",
and proceeds to convert away from the standard setting C2.
I am not complaining, as in fact this solved a bit of a mystery for me.
The diffraction images had originally been indexed as I222. Integration
proceeded without a hitch, but the data failed miserably to scale acceptably.
Running pointless immediately made clear what the problem had been.
Instead I am merely curious.
What are the criteria that pointless uses to decide such a thing?
In this case the beta angle is _very_ near to 90. I have fed other
C2 data sets to pointless and not seen even a mention of I2 in the
output. Is the "score" mentioned in the log file some weighted function that
says the closer beta approaches 90 after re-indexing, the more that
re-indexing is preferred?
Ethan
[*] Not least because I had never previously encountered "I2" as the
name of a spacegroup. Live and learn.
--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
