On Friday 08 May 2009 10:36:28 Phil Evans wrote:
> 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
A follow-up to this discussion.
I finished refinement, and I am ready to deposit with the PDB.
However, when I went to produce a *.cif file for deposition, I found
that mtz2various is confused by the I2 setting. It kept the cell
edges and angles from I2, but created a *.cif output file that claims
the cell is C2 and it lists the symmetry operators for C2.
I manually corrected the header records in the *.cif file, but the
program itself should be fixed as well.
I ran:
### CCP4 6.1: MTZ2VARIOUS version 6.1 : 12/11/08##
The mtz2various log file contains the line:
* Space group = 'I121' (number 5)
By contrast, running mtzdmp on the input file it is converting reports
* Space group = 'I 1 2 1' (number 4005)
cheers,
Ethan
> 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
