On Wed, 2012-01-18 at 16:54 +0000, Paul Emsley wrote: > On 18/01/12 10:47, Martyn Winn wrote: > > This needs a 1-line fix in syminfo.lib file. In the spacegroup entry > > (the second entry in the file), replace: > > > > symbol old 'P -1' > > > > with > > > > symbol old 'P 1-' > > > > This works for me at least. The syminfo.lib file can be found in: > > .../coot-whatever/share/coot/syminfo.lib > > or in: > > .../ccp4-whatever/lib/data/syminfo.lib > > > > Yes, it is an mmdb issue, in that mmdb tries to match the spacegroup in > > the CRYST1 card against the spacegroups in syminfo.lib (it checks > > against "symbol xHM" and "symbol old" entries). > > > > There are apparently a handful of centrosymmetric entries in the PDB, > > e.g. racemic mixtures of synthetic peptides. Actually, looking at the > > spacegroups offered in the RCSB advanced search menu, "P 1-" is the only > > case. > > > > Clearly, it is "only" a matter of convention whether you use "P -1" or > > "P 1-" .... > > > > Thanks for looking into this Martyn. > > So just to be completely clear, CCP4 is changing symbol old for P -1 in > symop.lib? > > Paul.
I have changed it in syminfo.lib not symop.lib That is what mmdb uses nowadays, and seems to be what you distribute. I have CVS'd the change into the CCP4 repository, and I presume it will appear in the next release. Sue Roberts pointed out to me that CCDC write out "P -1". syminfo.lib now has: symbol xHM 'P -1' symbol old 'P 1-' which should cover both cases (mmdb checks against both xHM and old). m -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: [email protected] * * Fax: +44 1925 603634 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***********************************************************************
