-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 In ccp4-6.3.0, the chiral volume of SO4 is marked as 'both'. SO4 chir_01 S O1 O2 O3 both
Tim On 07/11/12 12:39, Robbie Joosten wrote: > 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: > > 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/Vt+UxlJ7aRr7hoRAu3aAJ9lBBav5Fz9W310QZCA+8hBrvYyEACfe/wV a56yOVyYtgOODEN2ypSLMA0= =9yvs -----END PGP SIGNATURE-----
