On Mon, Sep 06, 2010 at 02:45:49PM +0100, Martyn Winn wrote: > > 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 ...
What good old days were those? The Cryst1-format for PDB-files in the ccp4 documentation says 56-66 Space group symbol, left justified (not used) which is eleven characters. Were there days when this was different? Tim > > 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/ * > *********************************************************************** -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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