Dear IMP,
I recently started playing around with IMP and was thinking that it would be great to be able to specify secondary structures, especially helices instead of beads. So for example if I have a homology model for a domain or two and want to model the full length protein, I would specify the rest of sequence as beads of some size in the topology file. However if I had a reasonably confident prediction of helices, I could specify what would be essentially "rods" instead of "beads". It seems to me that might help get the geometry right in some situations. I do see that there's a way to add_representation(mol, resolutions=[1,10], ideal_helix=True) but don't quite see how I can wedge that into a multiscale topology of a model.
Thanks much, Julian