2009/10/8 Dina Schneidman duhovka@gmail.com
> I used "introduction to protein structure" branden &tooze as a source > (nice book!). If I remember correctly the same story appears in > biochemistry textbooks. > > The very same definition, put it in extreme terms, will allow us to call a entire fiber of "proteins" in the cell as one protein (think about filaments, etc), something that I've seen nobody doing. I guess that the definition is kind of loose, but is not going to help us, in terms of our software, to call a PROTEIN to something that has a big number of chains. I would slightly prefer complex[1].protein[1] than protein[1].chain[1], but not enough to discuss it too much.
> > > > > > 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 > > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >