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