My guess is that they are not listed consecutively in the pdb file. That is, in the PDB it is Protein A Protein B Zinc A Zinc B It would be easy enough to modify the pdb reader to merge chains as they are encountered if that seems appropriate.

However, in general, I would suggest using an IMP.atom.Selection for navigating the hierarchy. If you do that it won't make much difference whether there are two separate chain particles or one. That said, not all bits of IMP work naturally with the Selection model.

On Apr 4, 2011, at 1:13 AM, Benjamin SCHWARZ wrote:

> Hi list, > > Using read_pdb, I expected it to return a hierarchy with distinct chains that could be plainly distinguished solely on their chain ID, this seems not to be the case, and I don't know wether this is a desired behavior or a minor bug. > > As an exemple, pdb structure '1pgu' contains : > - two protein chains, A and B > - two Zinc ions (one of them being attached to chain A and the other to chain B) > - and water molecules attached to both chains. > When read through read_pdb, the hierarchy contains 4 children, all 4 eligible for a "conversion" to Chain, each Zinc ion being considered as a chain. I thus have two chains A and two chains B in the hierarchy. > > --Ben.S. > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users