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
