On Nov 1, 2009, at 11:03 PM, Javier Ángel Velázquez Muriel wrote:

> > Hi. I'm testing IMP with a PDB file that has 3 models inside, and is > quite big: ~900 kDa, 60 chains. I was expecting problems with > reading more than one model, but I'm also getting this: > > ERROR: Can only allocate 150000 particles. Yell at Daniel. As it says, there is currently a limit on the total number of particles. I can increase it if needed as, apparently, is needed.

> > 1) Can IMP read multi-model PDBs now ? The code seems that it can. It has a flag to read one or all models, but I'm not sure that the reading all option is very useful.

> 2) How are the models treated? One IMP model per PDB model ? I would > like to have all the PDB models into the IMP model in this case. Everything always goes into the same model (since the read_pdb function only takes one model as an argument). It currently just produces a atom.Hierachy node with all chains and molecules from all models as children, making sorting things out a bit annoying (as was discussed in the meeting on pdb reading).

> 3) How does IMP identify chains internally? How can I access chain > 54, for example, given that it's name is repeated in the PDB file? > (The PDB has 3 models, 20 chains each, repeated name). They will just be repeated in the model. Not necessarily very useful.

It is probably worth producing a separate "read_all_models_from_pdb" which produces a more structured output (say a vector of Hierarchies, one per model). That would be quite easy. If we do that, we should remove the read all models flag from the existing read_pdb.