Eric, Thanks for the answer. I was aware of the 'sequences' method but I needed singleton residues as well, which is the reason why I tried implementing my own chain detection. So I went with your solution 2 using the rootForAtom(atom, True) method and it did the trick! Thanks again, Sebastien 2009/7/20 Eric Pettersen <pett@cgl.ucsf.edu>
Hi Sébastien, You don't precisely say why you need to know if two residues are in the same chain, so I'm going to describe two solutions. If they aren't sufficient for your needs then let me know why and I can offer further suggestions. Anyway:
solution 1) Molecules have a 'sequences()' member function that returns a list of Sequences. These Sequences are the multi-residue chains (*i.e.* there is no Sequence containing waters). Each Sequences has a 'residues' attribute which is the list of Residues in the chain. So you can easily run through the residues of a chain this way.
solution 2) For purposes of drawing the graphics, each connected chain of atoms has a unique "root" atom that drawing commences from. Therefore if "a1, a2 = res1.atoms[0], res2.atoms[0]" then res1 is in the same connected chain as res2 if "res1.molecule.rootForAtom(a1, True) == res2.molecule.rootForAtom(a2, True)". The second argument to rootForAtom() controls whether the chain is considered connected across active bond rotations.
bonus solution :-) ModelPanel.base has a getPhysicalChains function that return a list of lists. Each list is residues in the same physically connected chain, though the first list is singleton residues.
--Eric
On Jul 20, 2009, at 6:30 AM, Sébastien Cuendet wrote:
Hi,
I'm working with PDB files, opening them with:
chimera.openModels.open(fileHandler, 'PDB').
Later on when I use the chainId on the residues of the molecule (accessed by residue.id.chainId). The problem is that the PDB format does not require the chaind id to be defined. When that is the case, all residues have id ' ', which is rather annoying to distinguish the chains to which they belong.
Now, bringing up problems only is never really appreciated ;), so my colleague Aurelien Grosdidier and I tried to think of some solutions to split the residues into chains when loading a model from a PDB file that does not contain any chain ID.
1) Split on TER. Chains are usually separated by a TER line, which could thus be used to determine when to create a new chain. However, like the chain id information, the TER line is optional in the PDB format...
2) Compute an atom to atom distance matrix for each two consecutive residues. Since the typical distance between two atoms is known, we can compute if two residues reasonably belong to the same chain. The computations can easily be pruned when two residues belong to the same chain, which is the most frequent case.
3) Compute an atom to atom distance matrix and use it to determine which atoms belong to the same chain. This is computationnally more expensive than 2), but it must be done somewhere in Chimera to compute the bonds between the atoms that are rendered graphically. Any chance we can access this information (I did not find how)?
Any comment on those solutions? Any other solutions? Any help will be appreciated!
Thanks,
Sebastien _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev