hchoe wrote: > I have used the following subroutine to define tetramers in > symmetry. Please tell me how to do it in MODELLER8v0.
See http://salilab.org/modeller/manual/node159.html for a general example. In your specific case, you could translate your TOP script line for line to Python; alternatively, you could take advantage of Python's own loop constructs and use something like the following, which is a little more flexible:
def defsym(mdl): segs = (('323:', '608:'), ('609:', '894:'), ('895:', '1180:'), ('37:', '322:')) for ind in range(len(segs)): for (set, seg) in ((2, segs[ind-1]), (3, segs[ind])): mdl.pick_atoms(res_types='ALL', atom_types='MNCH', selection_status='INITIALIZE', selection_search='SEGMENT', pick_atoms_set=set, selection_segment=seg) mdl.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False))
One notable difference is that the old TOP scripts could only act on a single model. In Modeller 8v0 there is no limit to the number of simultaneous models (other than system memory) and hence you must identify which model you wish the defsym routine to act upon (this is the mdl argument).
Ben Webb, Modeller Caretaker