Query about structural alignment of a homopentamer with salign
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:
log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files']
aln = alignment(env) for (code, chain) in (('4cof_extracelular', 'A'), ('4cof_extracelular', 'B'), ('4cof_extracelular', 'C'), ('4cof_extracelular', 'D'), ('4cof_extracelular', 'E'), ('glucl', 'A'), ('glucl', 'B'), ('glucl', 'C'), ('glucl', 'D'), ('glucl', 'E')): mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=code+chain)
for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), ((1., 0.5, 1., 1., 1., 0.), False, True), ((1., 1., 1., 1., 1., 0.), True, False)): aln.salign(rms_cutoff=3.5, normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='tree', # If 'progresive', the tree is not # computed and all structues will be # aligned sequentially to the first #ext_tree_file='1is3A_exmat.mtx', # Tree building can be avoided # if the tree is input feature_weights=weights, # For a multiple sequence alignment only # the first feature needs to be non-zero improve_alignment=True, fit=True, write_fit=write_fit, write_whole_pdb=whole, output='ALIGNMENT QUALITY')
aln.write(file='1is3A.pap', alignment_format='PAP') aln.write(file='1is3A.ali', alignment_format='PIR')
# The number of equivalent positions at different RMS_CUTOFF values can be # computed by changing the RMS value and keeping all feature weights = 0 aln.salign(rms_cutoff=1.0, normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='progressive', feature_weights=[0]*6, improve_alignment=False, fit=False, write_fit=True, write_whole_pdb=False, output='QUALITY').
Thank you in advance for your help, Ivan Felsztyna
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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Iván Felsztyna -
Modeller Caretaker