ok - fair enough .... all the proteins I worked with so far had a single chain :) 1. by Root you mean Protein? 2. Fragment is a good level to have, so I vote we keep it.
Just to engage others in the discussion, the current atom hierarchy is:
** \name Hierarchy Types The various valid levels for the atom Hierarchy: - ATOM (0) an atom - RESIDUE (1) a residue - NUCLEICACID (2) a nucleic acid - FRAGMENT (3) an arbitrary fragment - DOMAIN (4) a chain of a protein - CHAIN (5) a chain of a protein - PROTEIN (6) a protein - NUCLEOTIDE (7) a nucleotide - MOLECULE (8) an arbitrary molecule - ASSEMBLY (9) an assembly - COLLECTION (10) a group of assemblies - UNIVERSE is all the molecules in existance at once. - UNIVERSES is a set of universes - TRAJECTORY is an ordered set of UNIVERSES
On Oct 8, 2009, at 8:35 PM, Dina Schneidman wrote:
> 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 >> > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev