In fact it's not quite true to say that the symm ops are used as the
definitive source of space group information in all circumstances: where
the SG info is read from some types of file (e.g. MTZ header), but by no
means all (e.g. PDB files don't contain symm ops), then it appears that
at least in some cases the symm ops take precedence. However some
programs don't read a file containing the symm ops and neither do they
expect the user to supply the symm ops, because it's clearly much more
convenient (and much less error-prone!) to ask the user to type in the
SG number or name, and then do a look-up in syminfo.lib for the symm
ops. It seems to me that's entirely reasonable - what would you say if
a program asked you to type in (interactively) the symm ops for a cubic
space group!
Cheers
-- Ian
> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
On
> Behalf Of George M. Sheldrick
> Sent: 11 June 2009 17:17
> To: [log in to unmask]
> Subject: Re: [ccp4bb] mtz2various is broken [ was: Another pointless
> question ]
>
> Using the symmetry operators as the definitive source of space group
> information, rather than the name or number of the space group, is the
> only completely safe approach, and I am pleased to see that CCP4 now
> does this. SHELX has worked this way since 1970, though in a moment of
> weakness I allowed the space group name to be input to shelxc.
>
> George
>
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-3021 or -3068
> Fax. +49-551-39-22582
>
>
> On Thu, 11 Jun 2009, Kevin Cowtan wrote:
>
> > 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
> >
> >
Disclaimer
This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [log in to unmask] and destroy all copies of the message and any attached documents.
Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
|