If refmac requires comment after chem_comp it is a bug. It needs to be fixed. I will try to fix it for next version - 5.7 series.
Garib On 30 Nov 2011, at 16:08, Ian Tickle wrote: > Note that the _chem_comp and _chem_comp_tor blocks are formatted the > same way if there's only one compound/torsion resp. e.g.: > > _chem_comp.id XXX > _chem_comp.three_letter_code XXX > _chem_comp.name XXX > _chem_comp.group . > _chem_comp.number_atoms_all 7 > _chem_comp.number_atoms_nh 4 > _chem_comp.desc_level . > # > > _chem_comp_tor.id other-001 > _chem_comp_tor.atom_id_1 CL > _chem_comp_tor.atom_id_2 C > _chem_comp_tor.atom_id_3 N > _chem_comp_tor.atom_id_4 H1 > _chem_comp_tor.value_angle 0.0 > _chem_comp_tor.value_angle_esd 1000000.0 > _chem_comp_tor.period 10 > > Just as a matter of interest, I take it that Refmac, Libcheck, > Sketcher etc all accept this fprmat? I agree that if it's using a > proper CIF reader it should be able to handle this without blinking. > I'm pretty sure Refmac doesn't (or didn't when I tested it some time > ago, maybe it's been fixed), because it requires that the _chem_comp > block (only) be terminated by a comment line (as in the example): > that's definitely not in the spec. > > Cheers > > -- Ian > > On 30 November 2011 15:34, Judit Debreczeni <[email protected]> > wrote: >> On 30 November 2011 15:06, Paul Emsley <[email protected]> wrote: >>> On 30/11/11 10:52, Judit Debreczeni wrote: >>>> >>>> Grade (from Global Phasing) produces cif files with non-loop_ >>>> descriptions of chiral restraints, e.g.: >>>> >>>> _chem_comp_chir.comp_id INH >>>> _chem_comp_chir.id chir_01 >>>> _chem_comp_chir.atom_id_centre C1 >>>> _chem_comp_chir.atom_id_1 C >>>> _chem_comp_chir.atom_id_2 C2 >>>> _chem_comp_chir.atom_id_3 O >>>> _chem_comp_chir.volume_sign negativ >>>> >>>> >>>> This format seems correct to me and actually makes a lot of sense if >>>> there is only one chiral centre in the molecule. >>>> >>>> Coot, however, ignores such records entirely, so the chirality remains >>>> unrestrained, cannot be edited in the restraints editor or flipped by >>>> a keystroke. Using 0.7-pre-1 (revision 3792) [with guile 1.8.7 >>>> embedded] [with python 2.7.0 embedded]. >>>> >>>> Bug? Oversight? Feature? >>>> >>>> >>> >>> Oversight. I didn't think that anyone would be so contrary as to format >>> their chirality in such a way (it seems to me that they must have gone out >>> of their way to do so - I wonder why...) >>> >> >> >> Contrary? -- We are talking about the genuine and vanilla RCSB cif >> parser which I thought should be the gold standard? >> >> >>> Anyway, it's something that I should fix. I'll add it for 0.7. >>> >> >> >> Thanks. >> >> JED. >>
