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?
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>>>>
>>>
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