Hi Joel,
I prefer the swapping of atom names, which is pretty much what the program chiron does, over hacking the restraint file. The latter makes the problem reappear as soon as you use your PDB file on a machine with an 'unhacked' restraint file. @Ian: You'd be surprised how well Refmac can flatten sulfates if you have a chiral volume outlier (see Figure 1d in Acta Cryst. D68: 484-496 (2012)). Cheers, Robbie From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Wednesday, July 11, 2012 12:15 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Chiral volume outliers SO4 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 <tel:%2B64%203%20479%207293> > > - -- - -- 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-----
