Protein is more than a chain. Chain corresponds to tertiary structure. Protein's quaternary structure can have more than one chain! A classic example is hemoglobin, 4 chains. Another classics is antibody, 2 chains. So we need chains around! and also how can we add bonds without chains? do you plan to connect them together?
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.
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 >