On Tuesday 09 June 2009 02:45:41 Ian Tickle wrote:
>
> Ethan - that's odd it works for me (CCP4 6.1.0) unless of course it got
> broken recently in 6.1.1:
I see the same problem in both 6.0.2 and 6.1.1.
I don't have a copy of 6.1.0 around to test.
Your version fails to convert space group "4005" to "5".
I am running 6.1.1 built from the source tarball.
This version does convert "4005" to "5", but then it makes the
mistake in subroutine wcifhr(mtzin,iun,dbhead) of calling
C--- Change short H-M symbol to full CIF-style symbol:
call MSYMLB3(24,nspgrx,spgrnx_cif,spgrnx_cifs,pgnamx,
& nsympx,nsym,rsym)
which looks up the space group name and symops based on the converted number.
Having done that, it now thinks the space group is C2, even though
the cell parameters and reflection indices are not correct for that
setting.
So both versions are broken, but in different ways.
I have not been able to track down which routine in which source file
was changed. But since I see the same problem in 6.0.2, I'm not sure there
_is_ a difference in the source files I have on hand. Is it possible that
this was partially fixed for 6.1.0 but then reverted because of the problem you
report, leaving it broken again?
Ethan
> 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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--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742
