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?
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