hi daniel,
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) final_restraint = lower_scoring_one_of(rest1, rest2) model.add_restraint(final_restraint)
(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.
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Friedrich Foerster Max-Planck Institut fuer Biochemie Am Klopferspitz 18 D-82152 Martinsried
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