2009/10/8 Daniel Russel drussel@gmail.com
> > 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. >> > That is what I always assumed :-) > > So we need chains around! and also how can we add bonds without >> chains? do you plan to connect them together? >> > No one said anything about getting rid of chains. Just about getting rid > the PROTEIN/CHAIN distinction. > > and let me put two more cents: >> PDB format does not define any hierarchy. it is a set of atoms. >> > It does too define a hierarchy: > a pdb file contains models > models contain chains and heterogens > chains contain residues > residues contain atoms > heterogens contain atoms > > if we >> want to build an hierarchy out of PDB it should clearly follow from >> the format. >> > I don't see that the second follows at all from the first. In fact I would > say quite the opposite. But I disagree with the first, so it doesn't really > matter :-) > > 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. >> > Plus the parallel various ligands and stuff which also need to get attached > to root (preventing root from being a protein or molecule). > > To put one of the problems another way, the big problem is that, > ultimately, one would like a hieararchy with a molecule (protein) containing > multiple chains.
Perhaps not the best source, but wikipedia says:
In biochemistry http://en.wikipedia.org/wiki/Biochemistry, *quaternary structure* is the arrangement of multiple foldedhttp://en.wikipedia.org/wiki/Protein_folding protein http://en.wikipedia.org/wiki/Protein molecules in a multi-subunit complex.
1 protein = 1 chain. more chains = complex.
> The PDB reader can't, in general, create such a thing since it doesn't know > how the chains are grouped into molecules. As a result, it has to return > something intermediate.
True
> Currently it returns a hierarchy would would have to be broken apart and > put back tother in order to get the presumably desired result.
True
> I would suggest producing a vector of molecules instead so that the user > can filter them/assemble them as needed.
Yes
> We could provide special versions of the reader to handle easy cases (like > where you know the pdb file only contains one protein). > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >