Re: [modeller_usage] specify sequence ranges for salign/align2d

[Modeller Caretaker <>]

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
--
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