I2 is always an alternative setting to C2, & Pointless (by default)
will choose this (since 1.2.12 I think) if it gives a smaller beta
angle than the C2 setting
I am assured that this is the IUCr approved "standard", along with
always setting primitive orthorhombic space groups with a < b < c even
if this makes eg space group 18 P 2 21 21. However, there are some
"old-fashioned" programs :-) which don't like this (arp/warp at
present for example, though I believe this will change in future), so
Pointless does offer the option SETTING SYMMETRY-BASED, also an option
in the ccp4i GUI, to choose the "reference" setting and C2
Keeping the obliquity of the cell small has some advantages: it may
make map viewing easier, and improve the accuracy of map interpolation
in programs which are a bit casual about doing this properly
Phil
On 8 May 2009, at 17:45, Ethan Merritt wrote:
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
