Re: [modeller_usage] Query about structural alignment of a homopentamer with salign

[Modeller Caretaker <modeller-care@salilab.org>]

On 7/3/18 11:22 AM, Iván Felsztyna wrote:
> Hi, I'm trying to use the script salign_multiple_struc.py to obtain the 
> structural alignment of two homopentamers. I want to use them as 
> templates for a multi-template modelling. The problem is that the fitted 
> pdb files that I obtain include only one of the subunits of each of the 
> homopentamers, while I need the whole protein to be aligned. I copy here 
> the script:
Your for loop makes an alignment of 10 structures, each of which is a 
single chain, because you ask with model_segment to read from the first 
residue to the last residue of the same chain ID. You probably want 
something like this instead (assuming your chains A through E are 
ordered ABCDE in your two PDB files):
for (code, startchain, endchain) in (('4cof_extracelular', 'A', 'E'),
                                     ('glucl', 'A', 'E')):
    mdl = model(env, file=code,
                model_segment=('FIRST:'+startchain, 'LAST:'+endchain))
    aln.append_model(mdl, atom_files=code, align_codes=code)


	Ben Webb, Modeller Caretaker
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