Hi Martyn Since seeing Ethan's last posting I guessed immediately, following on from what Kevin had said earlier, that the program in Ethan's sequence which made the change from SG #4005 to #5 in the MTZ header (and my tests confirm this) is ctruncate; this behaviour presumably is a feature of the Clipper library, so I guess is common to all programs using Clipper (though pointless appears to be an exception - presumably because it specifically creates the 4005 code rather than simply transferring it from input to output). All the other programs in his sequence copy the SG #4005 unchanged.
So essentially the problem is an incompatibility between the old (c)symlib and the Clipper library; the former still uses the old conventions that 1) the SG number uniquely identifies alternative settings corresponding to a given standard setting, and 2) the SG number takes precedence over the SG name and/or symm ops to determine the space group, whereas the latter doesn't use unique numbers to identify alternative settings, and assumes the reverse precedence. You suggest changing MSYMLB3 to fix this, i.e. essentially changing it to conform to the symlib documentation (!), so that the SG name takes precedence over the number - I agree this ought to work. The only issue I see is that many programs (e.g. see several examples of this usage in SFALL documentation) allow user input of either the SG name or number, e.g. in SFALL, PDBSET etc: SYMM I2 and SYMM 4005 are equivalent. If we are going to move to the new Clipper-style convention I wonder how this would be handled, if the SG numbers no longer uniquely identify the setting. I guess we would lose this rather useful (IMO at least) feature! I assume you would at least continue to allow use of CCP4-style SG numbers via MSYMLB3 - all our internal scripts rely on this feature. Cheers -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of Martyn Winn > Sent: 12 June 2009 20:46 > To: Ethan Merritt > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] mtz2various is broken [ was: Another pointless > question ] > > Apologies, have been away. I hope I have extracted the relevant points > from this thread. > > For the record, the CCP4 library also uses the symops to determine the > spacegroup, when it can. Hence the observation below that mtzdmp and > refmac find the right spacegroup. > > However there are plenty of cases where the symops are not available, > PDB files with CRYST1 card only, user keywords, etc. And there is plenty > of independently developed application code which may not follow the > library (bearing in mind that we are an anarcho-syndicalist commune etc > etc). > > Ian is right that the surest way of checking the MTZ file is to open in > a text editor. You can also edit the SYMINF line this way, though this > is probably classed as advanced ccp4 usage... So in my tests > > SYMINF 4 2 I 4005 'I 1 2 1' PG2 > > works fine, while > > SYMINF 4 2 I 5 'I 1 2 1' PG2 > > shows the problem. And yes, the problem is then MSYMLB3 using the 5 > rather than the spacegroup name or the operators. We should be able to > fix that. > > 4005 is for internal usage, converting to 5 on export from the suite. > Probably the generating program should have used 4005. > > Cheers > Martyn > > > 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 > > > -- > *********************************************************************** > * * > * Dr. Martyn Winn * > * * > * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * > * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk * > * Fax: +44 1925 603825 Skype name: martyn.winn * > * URL: http://www.ccp4.ac.uk/martyn/ * > *********************************************************************** 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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