mtz2various seems to get the symm info correctly from the header using
LRSYMI but then it calls MSYMLB3 using the SG number '5' (and the
correct name 'I121') which will cause the SG name and the symm ops to be
overwritten with the wrong ones (i.e. those for 'C2'). Again the
problem here is that the number is taking precedence over the name.
That's the way it has been done historically and it always worked
before, because there has always been a 1-to-1 correspondence between
the number and symm ops (via symop.lib or syminfo.lib), and that has now
been broken. If we're now doing it differently, i.e. the symm ops
taking precedence where there's a conflict, then someone must take
responsibility to ensure that all programs are updated to use the new
convention. I've no idea whether the problem is only in mtz2various or
whether others are affected. From what Ethan said it sounds like some
programs (e.g. Refmac) have been updated.
It seems to me the easiest way to fix this is to ensure that the symm
info in the header is all consistent with syminfo.lib, which in this
case means ensuring that the SG number in the header is the traditional
CCP4 one, i.e. 4005 for I2. If most programs ignore this anyway as you
say then obviously it can't affect them. It just means that programs
writing a CIF file need to write the number mod 1000, but this is
trivial.
Just got George's response: I agree that using the symm ops is the only
safe way in the long term, but in the meantime we have to deal with the
fact that some programs are still using the numbers (or names).
Cheers
-- Ian
> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
On
> Behalf Of Kevin Cowtan
> Sent: 11 June 2009 16:56
> To: [log in to unmask]
> Subject: Re: [ccp4bb] mtz2various is broken [ was: Another pointless
> question ]
>
> Not sure if this is relevant, but all clipper programs (and I think
all
> programs wince 6.0) take the symmetry operators as the source for the
> spacegroup rather than the spacegroup symbol.
>
> So I would expect changing the spacegroup number or symbol would not
> affect most programs in any way.
>
> It is possible of course that there is a way to access the file symbol
> or number, in which case there may be a few programs which might be
able
> to get the wrong spacegroup from an inconsistent file.
>
>
> Ethan Merritt wrote:
> > On Thursday 11 June 2009, Ian Tickle wrote:
> >>> -----Original Message-----
> >>> From: Ethan Merritt [mailto:[log in to unmask]]
> >>> Sent: 11 June 2009 00:35
> >>> To: Ian Tickle
> >>> Cc: [log in to unmask]; Phil Evans
> >>> Subject: Re: mtz2various is broken [ was: Another pointless
question ]
> >>>
> >>> 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.
> >> I just compiled 6.1.1 mtz2various.f with 6.1.1 CCP4 libs & I get
> >> identical results (i.e. log & CIF files) with 6.1.0. Differences
> >> between the source versions are minor (related only to CIF line
> length).
> >> Also there are minor formatting differences betweeen 6.0.2 & 6.1.x,
but
> >> symmetry info is identical. So it's not a version issue, but must
be
> >> what's in the MTZ file header. Have you looked at the file header,
> does
> >> it contain the right symmetry operators? Most programs including
> >> mtzdump don't bother to print these out but blithely assume that
they
> >> are consistent: the mtztona4 program writes out the complete file
> header
> >> in ascii, or you can just open the MTZ file in a text editor (as
long
> as
> >> it doesn't mind the non-ascii characters and the long lines!).
Here's
> >> the relevant bit of mine:
> >>
> >> CELL 70.3025 68.7834 93.7125 90.0000 94.1913 90.0000
> >> SORT 1 2 3 0 0
> >> SYMINF 4 2 I 4005 'I2 ' PG2
> >> SYMM X, Y, Z
> >> SYMM -X, Y, -Z
> >> SYMM X+1/2, Y+1/2, Z+1/2
> >> SYMM -X+1/2, Y+1/2, -Z+1/2
> >> END
> >>
> >> If I change 'I2' to 'I121' to look like yours I still get the same
> >> results, so that's not the problem.
> >
> > My mtz file contains
> > CELL 148.6099 98.3798 251.9687 90.0000 90.3258 90.0000
> > SORT 1 2 3 0 0
> > SYMINF 4 2 I 5 'I121' PG2
> > SYMM X, Y, Z
> > SYMM -X, Y, -Z
> > SYMM X+1/2, Y+1/2, Z+1/2
> > SYMM -X+1/2, Y+1/2, -Z+1/2
> > RESO 0.0000607290094194 0.1371708661317825
> >
> > So there is a difference, but not the expected one.
> > My mtz file has exactly the info that should go into the cif
headers,
> > including the space group number of the standard setting: 5.
> > But mtzdmp and refmac, etc, do manage to find and report the
spacegroup
> > as 4005 from this same file.
> > Could there be two conflicting spacegroup numbers stored in the
header?
> >
> > For what it's worth. I see the same behavior on files created by
> > pointless (re-indexed from C2), files created directly by
> > mosflm/scala/truncate, and files merged by CAD.
> >
> > Ethan
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