Hi everybody -

I'm modelling a membrane protein and I have externally refined my helices. Now I want to have modeller build ab initio interhelical loops using modeller but my primary functional requirement is to keep the helices in the target exactly the same as the template. The default parameters for the model.build method aren't linking up the loops; the strands are just flying outwards from the helical bundle. I am guessing I need to define a whole set of restraints? Using anything other than INTERNAL_COORDINATES for build_method is making a complete mess of the model.

(I cannot use the automodel superclass because at the end, it is altering my helical structures in order to fit the loops.)

model.py:

log.verbose() env = environ() #all hydrogen model env.libs.topology.read(file='$(LIB)/top_allh.lib') env.libs.parameters.read(file='$(LIB)/par.lib')

#instantiate new alignment aln = alignment(env) aln.append(file='assem.ali', align_codes=('or17209h_helix', 'or17209h')) #instantiate new model mdl = model(env) mdl.generate_topology(aln, sequence='or17209h') #xfer the template coords mdl.transfer_xyz(aln) #build ab initio loops mdl.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') mdl.write(file='test.ini')

The way the .ali is arranged is that the template has the loops gapped out, and the sequence is the complete protein.

Any ideas on how to get the loops to connect? I don't care about optimization since I will be running MD in parameterized solvent anyway.

TIA Peter