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?
Perhaps not the best source, but wikipedia says:
In biochemistry, quaternary structure is the arrangement of multiple foldedprotein 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 <">> 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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