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: [log in to unmask] *
> * 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
|