Douglas Kojetin wrote: > WIth reference to Tutorial 2 (Advanced Modeling): > > http://salilab.org/modeller/tutorial/advanced.html > > Is it possible to: > > (1) specify the sequence number ranges for the templates to be used in > the structural alignment within 'salign.py'? > > or > > (2) specify the sequence number ranges for the template or target to be > used in the sequence alignment within the script 'align2d_mult.py'?

Of course - both of these are straightforward.

For (1), just specify model_segment when you read in the model. The example you mention reads a whole chain for each PDB, but you can read whatever you like, e.g.

aln = alignment(env) mdl = model(env, file='foo.pdb', model_segment=('1:', '34:')) aln.append_model(mdl, atom_files='foo', align_codes='foo') mdl = model(env, file='bar.pdb', model_segment=('3:A', '95:B')) aln.append_model(mdl, atom_files='bar', align_codes='bar')

and so on... This makes an alignment of residues 1-34 from 'foo.pdb' against residues 3:A to 95:B from 'bar.pdb'.

For (2), you can give the residue range in the alignment file header. See http://salilab.org/modeller/manual/node176.html. The example there reads residues 1-106 for the 5fd1 structure, and 1-54 for the 1fdx sequence.

Ben Webb, Modeller Caretaker