Hi Paul, On Thu, 2011-12-01 at 14:24 +0000, Paul Emsley wrote:
> On 30/11/11 15:34, Judit Debreczeni wrote: > > > >>> Coot, however, ignores such records entirely, so the chirality remains > >>> unrestrained, cannot be edited in the restraints editor or flipped by > >>> a keystroke. Using 0.7-pre-1 (revision 3792) [with guile 1.8.7 > >>> embedded] [with python 2.7.0 embedded]. > >>> > >>> Bug? Oversight? Feature? > >>> > >>> > >> Oversight. I didn't think that anyone would be so contrary as to format > >> their chirality in such a way (it seems to me that they must have gone out > >> of their way to do so - I wonder why...) > >> > > > > Contrary? -- We are talking about the genuine and vanilla RCSB cif > > parser which I thought should be the gold standard? > > It took me a little while to understand what you meant. Yes, I suppose > that this could well be the "RCSB blessed" way of handling such > situations - and grade is merely following the rules. I take it back. The current STAR and CIF-family standards are in International Tables volume G. I have not found any distinction made between: # Form 1: Loop with exactly one packet loop_ _name1 _name2 value1 value2 and: # Form 2: <name> <value> pairs _name1 value1 _name2 value2 As far as I can tell, these two forms are exactly equivalent, and applications are free to choose whichever way they want to write the data out. An mmCIF could be written using only form 1 for all data. This might be a perverse choice from some points of view, but would not violate the standard. A conforming parser should handle both forms on input with identical outcomes. Any parser that only handles one of them has implicitly specified a dialect of (mm)CIF, and will be incompatible with software whose developer has chosen to only handle the other form. An application (like grade) that writes out mmCIF data then cannot satisfy both dialects simultaneously. The best it could do is have an option to control which dialect it writes out. It is far better that applications that read mmCIF's do so in a standards-conformant way. I don't think that this question has anything to do with the RCSB. I can't see any reason why they should prefer either form 1 or form 2, although someone else with more specific information may correct me here :-) > >> Anyway, it's something that I should fix. I'll add it for 0.7. Yes, that is clearly the best thing to do. I hope that this makes things clearer. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
