Re: [modeller_usage] tetramers in symmetry

[Modeller Caretaker <>]

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
--
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