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: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of George M. Sheldrick > Sent: 11 June 2009 17:17 > To: CCP4BB@JISCMAIL.AC.UK > 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:merr...@u.washington.edu] > > > > > Sent: 11 June 2009 00:35 > > > > > To: Ian Tickle > > > > > Cc: CCP4BB@jiscmail.ac.uk; 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. 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