Well - the problem may well be here - in the REFMAC dictionary (see $CLIBD/monomers.s.SO4.cif ) the chiral volume calculation uses at the order of the O numbering around the S atom . So if your O numbering is not right handed you will have the chiral volume calculated as positive, not negative.
There are various fixes. Edit the SO4 and just the numbering of 2 of the O atoms - eg use labels: S O2 O1 O3 Or edit the SO4.cif to have SO4 chir_01 S O1 O2 O3 both Eleanor loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign SO4 chir_01 S O1 O2 O3 negativ On 11 July 2012 10:59, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Joel, > > out of curiosity: what is "the Chiral volume outliers issue"? > > Cheers, > Tim > > On 07/11/12 01:00, Joel Tyndall wrote: > > Hi people, > > > > We are refining a structure with sulfates and we are getting the > > Chiral volume outliers issue. I understand the problem as being > > computational where the oxygens are in reality equivalent but > > computationally named differently. I have seen the recent Acta > > Cryst D paper (April 2012 - PDB_REDO) which talks about this issue > > and mentions the development of Chiron which could fix this issue. > > > > Is there a way to fix this problem using existing tools (or > > editing). > > > > We have ~20 sulfates in our protein (10-mer system) > > > > Thanks heaps > > > > Joel > > > > _________________________________ 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 > > > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFP/U5+UxlJ7aRr7hoRAqaUAKD4Eo2tqarIwbK6+mHIfYYHcyhAKQCgy02F > XK8ZYLNW3gI873nrtkZSv9E= > =ishS > -----END PGP SIGNATURE----- >
