HI Joe This and similar cases should be changed in the library from _chem_comp_chir.volume_sign = 'negative' (or 'positive') to 'both'. Then if you're concerned about the standardisation of the atom labelling you can always swap the labels of 2 atoms in the PDB file, but at least with 'both' non-standard labelling won't mess up the refinement. In this particular case the chiral specification seems somewhat redundant anyway since the geometry is completely nailed down by the 6 angle restraints! - so an even better solution might be to delete the _chem_comp_chir block entirely. You only need chiral restraints if one atom is a H (unless I suppose the density for the 4th atom is very poor). It would seem unlikely that the angle restraints would allow 'umbrella flips' if all 4 are non-H.
Cheers -- Ian On 11 July 2012 00:02, Joel Tyndall <joel.tynd...@otago.ac.nz> wrote: > Sorry I should have added, that the issue occurs following refinement in > refmac. (error in log file and SO4’s are distorted) > > > > _________________________________ > > Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry > National School of Pharmacy > University of Otago > PO Box 56 Dunedin 9054 > New Zealand > > Skype: jtyndall > > > > Ph: +64 3 479 7293 > >
