Daniel Russel wrote: > I was assuming the modeller reader was out for IP reasons
On the contrary, we should be using whatever we can from Modeller. If Modeller is in future determined to be deficient in some way, we can dump that functionality and write a new module in IMP, but if Modeller's up to the job, we should use it by all means. We're not setting out to rewrite everything from scratch - that would be silly.
> it would be great if someone could write a bridge for it > soon.
import modeller.scripts e = modeller.environ() e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') m = modeller.scripts.complete_pdb(e, "my.pdb")
after which all the coordinates are available in m.atoms[], all the bonds in m.bonds[], angles in m.angles[], etc.
Ben