Sorry a follow-up to this: the space-group number shown thus in the CIF
file:

_symmetry.Int_Tables_number      4005
_symmetry.space_group_name_H-M     'I 1 2 1'

should be shown as 5 NOT 4005!  SG nos > 230 are 'CCP4-isms', and
International Tables knows nothing about them!  I2 is merely an
alternative setting of space group no _5_.

Cheers

-- Ian

> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
On
> Behalf Of Ian Tickle
> Sent: 09 June 2009 10:46
> To: Ethan Merritt; [log in to unmask]; Phil Evans
> Subject: RE: mtz2various is broken [ was: Another pointless question ]
> 
> Ethan - that's odd it works for me (CCP4 6.1.0) unless of course it
got
> broken recently in 6.1.1:
> 
> First an extract from the mtz2various log file:
> 
>  * Cell Dimensions : (obsolete - refer to dataset cell dimensions
above)
> 
>    70.3025   68.7834   93.7125   90.0000   94.1913   90.0000
> 
>  *  Resolution Range :
> 
>     0.00030    0.24999     (     58.124 -      2.000 A )
> 
>  * Sort Order :
> 
>       1     2     3     0     0
> 
>  * Space group = 'I2' (number     4005)
> 
> 
> Then the CIF output:
> 
> ##########
> #        #
> #  CELL  #
> #        #
> ##########
> 
> 
> _cell.entry_id     junk
> _cell.length_a              70.3025
> _cell.length_b              68.7834
> _cell.length_c              93.7125
> _cell.angle_alpha           90.0000
> _cell.angle_beta            94.1913
> _cell.angle_gamma           90.0000
> 
> 
> ##############
> #            #
> #  SYMMETRY  #
> #            #
> ##############
> 
> 
> _symmetry.entry_id     junk
> _symmetry.Int_Tables_number      4005
> _symmetry.space_group_name_H-M     'I 1 2 1'
> 
> 
> ####################
> #                  #
> #  SYMMETRY_EQUIV  #
> #                  #
> ####################
> 
> 
> loop_
>  _symmetry_equiv.id
>  _symmetry_equiv.pos_as_xyz
>     1 'X,  Y,  Z'
>     2 '-X,  Y,  -Z'
>     3 'X+1/2,  Y+1/2,  Z+1/2'
>     4 '-X+1/2,  Y+1/2,  -Z+1/2'
> 
> The only thing I see is different is that your space group is shown as
> 'I121' whereas mine is just 'I2'
> 
> Hope this helps!
> 
> Cheers
> 
> -- Ian
> 
> > -----Original Message-----
> > From: [log in to unmask]
[mailto:[log in to unmask]]
> On
> > Behalf Of Ethan Merritt
> > Sent: 08 June 2009 21:56
> > To: [log in to unmask]; Phil Evans
> > Subject: mtz2various is broken [ was: Another pointless question ]
> >
> > 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
> 
> 
> 
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