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-" .... m On Tue, 2012-01-17 at 20:08 +0000, Paul Emsley wrote: > On 17/01/12 18:19, David Schuller wrote: > > Welcome to Coot. 0.6.2 (revision 3566) [with guile 1.8.8 embedded] > > [with python 2.7.2 embedded] > > Installed via yum: coot-0.6.2-8.20110715svn3566.fc16.x86_64 > > On Fedora 16 Linux > > > > I am trying to view a PDB file with a centrosymmetric space group. It > > doesn't seem to be working: > > > > In the file: > > CRYST1 29.302 23.215 23.184 72.96 90.60 90.60 P 1- 4 > > > > In the COOT log: > > Reading coordinate file: ****.pdb > > PDB file ****.pdb has been read. > > No Spacegroup found for this PDB file > > Cell: 29.302 23.215 23.184 72.96 90.6 90.6 > > ... > > No Symmetry for this model > > > > ========================== > > Either COOT does not support centrosymmetric space groups, or else it is > > not reading the space group identification properly from the standard > > CRYST1 line. > > > > OK, on further investigation, it is an mmdb issue - so most CCP4 > programs will fail similarly. > > IIRC, mmdb uses syminfo.lib for symmetry info - so if the symbol is > there, then symmetry is grokked. > > I don't think this is an issue for me to fix, it is an issue of general > concern to CCP4. Are all "P -?.*" space groups affected? (Mostly > rhetorical question). > > Maybe this is a PDB ploy to get us to switch to pdbx... :-/ > > Paul. -- *********************************************************************** * * * 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/ * ***********************************************************************
