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: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]
On
> Behalf Of Ethan Merritt
> Sent: 08 June 2009 21:56
> To: CCP4BB@jiscmail.ac.uk; 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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