Hi Andrew, Indeed, provided the atom labeling is correct the chiral volume restraint actually says whether the groups on the ring a axial or equatorial. The cif files do not define that any other way, so without the restraint the description of the molecule is ambiguous. Note that the chirality restraint only describes the hand, the actual chiral volume is calculated from the angle restraints.
In the more general case I think people are talking different languages. There is chemical chirality (the real deal) and computational chirality. In refinement and structure comparison the latter does matter (again, see Dale's post). Problems with restraints are one of the reasons why there are relatively many problems with ligands in the PDB (e.g. http://www.springerlink.com/content/eu28538101v7v885/). Cheers, Robbie > -----Original Message----- > From: Andrew Purkiss [mailto:a.purk...@mail.cryst.bbk.ac.uk] > Sent: Friday, July 13, 2012 14:09 > To: Robbie Joosten > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Chiral volume outliers SO4 > > Dear Robbie and ccp4bb, > > Is 1N1 not a different type of problem though, where a chirality restraint is > valid and so the atom labelling is important? > > Are you saying that we should always use the cif dictionary, even when there > are errors? Surely in the SO4 case, as Ian said, it is better to remove the > unnecessary restraint altogether. The sulphate cif file seems to have had this > bug introduced in the current CCP4 version. > > Andrew > > On Fri, 2012-07-13 at 12:54 +0200, Robbie Joosten wrote: > > Dear All, > > > > I'm with Dale on this one. It's better to have a standard and roll > > with it, than allow for ambiguity. The discussion just happened to > > start with a rather silly example as Tim pointed out. The ligand 1N1 > > (http://ligand-expo.rcsb.org/reports/1/1N1/1N1_D3L1.gif) is a better > > example: > > The atoms N5 and N6 can have inverted chirality. If it is just one of > > the two, then the molecule is distorted (IFF the restraint file is > > correct!). If both have inverted chirality than the problem can be > > fixed by label swapping. Hacking the restraint file to allow both > > positive and negative chirality would allow you to distort the molecule. > > > > Cheers, > > Robbie > > > > -- > Andrew Purkiss > X-ray Laboratory > London Research Institute > Cancer Research UK >
