Yes, I can reproduce this, and I think I have found the bug. It is simply that PDBSET dimensions the spacegroup name to 10 characters. Increasing that to 20 allows you to use either
spac 'F d -3 m :1' or spac 227 However, it still won't recognise 'F d -3 m' because this is not in the syminfo file (at least, not in a field that is read). There seem to be a few CCP4 Fortran files that have character spgnam*10 from the good old days ... Cheers Martyn On Mon, 2010-09-06 at 13:38 +0200, Tim Gruene wrote: > Hello, > I tried to assign a cell with space group F d -3 m to a PDB file using pdbset. > Since it did not recognize the string 'F d -3 m' (nor 'F d -3 m :1') , I used > the space group number 227. This resulted in the space group string 'F d -3 m > :' > in the PDB-file instead of 'F d -3 m :1' as it is listed in syminfo.lib, and > hence coot refused to display the symmetry mates for the molecule. > > When I add the missing '1' in the resulting PDB-file, coot does display the > cell, but when I ask to display the symmetry mates, coot chokes and consumed > all > my cpu power (for 8 molecules present in the unit cell...) until I killed it. > > I was wondering if this is a known bug in syminfo.lib (and/or the dependent > programs) and if there is a way around it (without using > phenix.get_me_out_of_here, I could of course use xp instead of coot for such a > small molecule). > > Kind regards, Tim > > P.S.: The bug in pdbset persits also in pdbset from ccp4-6.1.3 > -- *********************************************************************** * * * 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/ * ***********************************************************************
