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. >
