the Model hierarchy is not particularly awkward by itself. for me the
problem is more that dealing with a single hierarchy on the
representation level is hard.
i just constantly run into the problem that i want to press all my
restraints and representation into a single hierarchy - and i always
need to change it. so my hierarchy is basically just protein ->
fragment. whether a fragment is an atom, few residues, a domain, or an
entire protein varies from case to case. of course, i could add
another layer - but it'd be quite a bit of work to change it
everywhere and probably i'd need to change it again very soon.
for me a convenient framework for restraints would probably look like
that:
rest1 = upper_distance(particles_from_protein_A,
articles_from_protein_B)
rest2 = upper_distance(particles_from_protein_A,
articles_from_protein_C)
(protein_B and protein_C are both of the same protein type, e.g.,
lysozyme ). for tricky cases one could use several instances of
lower_scoring_one_of.
just a proposal....
cheers
frido
On Dec 19, 2008, at 2:02 PM, Daniel Russel wrote:
By the way, what exactly do you five cumbersome with the hierarchy
as it stands? Why do you find you are changing it a lot? Just
looking for ways to make things simpler.