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Re: [modeller_usage] enforcing symmetry in loop refinement



Mike White wrote:
I have modeled a homopentamer using automodel with enforcing pentameric
symmetry, and everything looks fine. There are two regions of each
subunit that have 3 and 5 residue long loops that aren't in the
templates. When I do loop modeling of all 10 of these loops at the same
time using a script based on the one in the Advanced tutorial, I get a
set of models where the loops are no longer symmetric.
I then introduced the same symmetry constraints in the loop modeling
that I used in the original model, and it produced models with the
appropriate symmetry. However, it took much longer (765 seconds of cpu
time to generate 5 loop models without the symmetry , but 8629 seconds
to generate 2 loop models with symmetry). I don't mind letting things
run overnight to generate models, but the hugh increase in computational
time suggests that I might not be doing this right.

Your script looks fine to me. Symmetry restraints are certainly going to be expensive to calculate, because they require calculation of all interatomic distances, d(ij). See http://salilab.org/modeller/manual/node251.html. The loop modeling potential, on the other hand, only works on nonbonded interactions, which are limited by the nonbonded pair list and exclude bonded atoms.

One way you can speed this up is to only constrain a subset of atoms. For example, you could constrain the backbone, or even just the C-alpha atoms, to be symmetrical. Simply change atom_types from 'ALL' to 'MNCH' or 'CA'.

	Ben Webb, Modeller Caretaker
--
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