I used "introduction to protein structure" branden &tooze as a source (nice book!). If I remember correctly the same story appears in biochemistry textbooks.
> > Perhaps not the best source, but wikipedia says: > > In biochemistry, quaternary structure is the arrangement of multiple folded > protein molecules in a multi-subunit complex. > > 1 protein = 1 chain. > more chains = complex. > >> >> and let me put two more cents: >> PDB format does not define any hierarchy. it is a set of atoms. if we >> want to build an hierarchy out of PDB it should clearly follow from >> the format. So the best way is to have 4 levels that are well defined >> by the corresponding PDB fields: >> Atom, Residue, Chain, Root >> I think all other assumptions are only assumptions and a good source for >> bugs. >> > > The problem is that root is not well defined either. We can agree on how to > define it, but please please please avoid the name UNIVERSE. Otherwise I'm > going to decorate all my universes with decorators called God. > >> On Thu, Oct 8, 2009 at 6:41 PM, Keren Lasker kerenl@salilab.org wrote: >> > sounds good to me >> > On Oct 8, 2009, at 6:35 PM, Daniel Russel wrote: >> > >> >> >> >> On Oct 8, 2009, at 6:32 PM, Keren Lasker wrote: >> >> >> >>> ok - if you mean that Chain should not be part of the Hierarchy, I >> >>> guess >> >>> it makes sense, as usually protein == chain. >> >> >> >> To make things clear, I'm using the IMP names, so CHAIN, PROTEIN are >> >> HierarchyTypes and Chain is a decorator. So there would not be a CHAIN >> >> hierarchy type, but a PROTEIN could be a Chain (if it has a chain >> >> designator). Sounds a bit icky... >> >> >> >>> On Oct 8, 2009, at 6:15 PM, Keren Lasker wrote: >> >>> >> >>>> for me more then one chain is an assembly ( or complex) >> >>>> I would leave Chain because in modeling sometimes people takes >> >>>> domains >> >>>> from different places ( with different chain ids) and this >> >>>> information might >> >>>> be useful. >> >>>> On Oct 8, 2009, at 6:13 PM, Daniel Russel wrote: >> >>>> >> >>>>> Does it make sense to talk about a protein which consists of more >> >>>>> than >> >>>>> one chain? I've heard people use the words that way (and there are >> >>>>> google >> >>>>> hits, but not a huge number), but it was suggested that this is a >> >>>>> misuse of >> >>>>> the words. It would make the atom hierarchy a bit simpler to say a >> >>>>> protein >> >>>>> is a single chain and has HierarchyType PROTEIN (and to remove the >> >>>>> CHAIN >> >>>>> type). >> >>>>> >> >>>>> Authoritative answers? Votes? >> >>>>> _______________________________________________ >> >>>>> IMP-dev mailing list >> >>>>> IMP-dev@salilab.org >> >>>>> https://salilab.org/mailman/listinfo/imp-dev >> >>>> >> >>> >> >>> _______________________________________________ >> >>> IMP-dev mailing list >> >>> IMP-dev@salilab.org >> >>> https://salilab.org/mailman/listinfo/imp-dev >> > >> > _______________________________________________ >> > IMP-dev mailing list >> > IMP-dev@salilab.org >> > https://salilab.org/mailman/listinfo/imp-dev >> > >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >