Hi Tom,

Apologies, I must have switched the numbers as I typed. The EM density is EMD-6271 and EMD-6270. If you fetch 6270 with fitted PDB's, it should be fairly obvious what I mean when it comes to fitting 2 different rings of proteins, however I wish to do this with my own structures in to their map, rather than the structures they have.

The structures I have a simulations/homology models, so they don't contain any BIOMT/symmetry information, thus I think I'm left with the only option being fitting each protein individually. Since I plan to do this quite a lot, I'd rather not have to resort to doing it by hand (and if it can be scripted - all the better).

I envisage the problem like this (correct me if you think this approach won't work though):

1. Open the first protein. Fit the first protein for each ring (1 monomer)

2. Continue to open models consecutively (or copy the existing one)

3. With each new model that is opened, fit it, but somehow determine if the same space is occupied with another model, if so, try elsewhere

I believe the fit-in-map function can be given a random starting position, such that fitting in to different densities could be achieved without manual initial placement. I think the conceptual step I'm stuck on would just be knowing whether chimera has any means of knowing whether 2 PDBs are occupying the same space (and/or EM density) - and then effectively using this as a conditional to re-attempt placement?

Thanks for the help thus far,

Joe