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 <">> 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