Hello, Modeller:
I try to do a multiple structural alignment using the example of "salign.py" script. The command went through, but the alignment file only contained the last template sequence. I have attached my script and the alignment files generated.
My pdb files containe only single chain. I can't figure out what could be wrong with my script. Why it always return the last template sequece. I use modeller 8v1. Thank you very much for your help!
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log.verbose()
env = environ()
env.io.atom_files_directory = "./:../atom_files/"
aln = alignment(env)
for (code) in (('2HI4-1A2'), ('1PQ2-2C8A'), ('1OG5-2C9A')):
mdl = model(env, file=code, model_segment=('FIRST:@', 'END:'))
aln.append_model(mdl, atom_files=code, align_codes=code)
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_cutoffs=(3.5, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60),
normalize_pp_scores=False,
rr_file='$(LIB)/as1.sim.mat', overhang=30,
gap_penalties_1d=(-450, -50),
gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0,
dendrogram_file='1is3A.tree',
alignment_type='tree', # If 'progresive', the tree is not
# computed and all structues will be
# aligned sequentially to the first
#ext_tree=True, # Tree building can be avoided if the tree
# is input
#input_weights_file='1is3A_exmat.mtx',
feature_weights=weights, # For a multiple sequence alignment only
# the first feature needs to be non-zero
improve_alignment=True, fit=True, write_fit=write_fit,
write_whole_pdb=whole, output='ALIGNMENT QUALITY')
aln.write(file='test1a.pap', alignment_format='PAP')
aln.write(file='test1a.ali', alignment_format='PIR')
aln.salign(rms_cutoffs=(1.0, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60),
normalize_pp_scores=False, rr_file='$(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')
>P1;1OG5-2C9A
structureX:1OG5-2C9A: 30 :A: 490 :A:undefined:undefined:-1.00:-1.00
PPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSGRGIFPLAE
RANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASPCDPTFILGCAPCNVIC
SIIFHKRFDYKDQQFLNLMEKLNENIEILSSPWIQVYNNFPALLDYFPGTHNKLLKNVAFMKSYILEKVKEHQES
MDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGAGTETTSTTLRYALLLLLKHPEVTAKVQEEIER
VIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPTSLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNP
EMFDPHHFLDEGGNFKKSKYFMPFSAGKRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASV
PPFYQLCFIPV*
_aln.pos 10 20 30 40 50 60
1OG5-2C9A PPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSG
_consrvd
_aln.pos 70 80 90 100 110 120 130
1OG5-2C9A RGIFPLAERANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASP
_consrvd
_aln.pos 140 150 160 170 180 190 200
1OG5-2C9A CDPTFILGCAPCNVICSIIFHKRFDYKDQQFLNLMEKLNENIEILSSPWIQVYNNFPALLDYFPGTH
_consrvd
_aln.pos 210 220 230 240 250 260
1OG5-2C9A NKLLKNVAFMKSYILEKVKEHQESMDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGA
_consrvd
_aln.po 270 280 290 300 310 320 330
1OG5-2C9A GTETTSTTLRYALLLLLKHPEVTAKVQEEIERVIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPT
_consrvd
_aln.pos 340 350 360 370 380 390 400
1OG5-2C9A SLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNPEMFDPHHFLDEGGNFKKSKYFMPFSAG
_consrvd
_aln.pos 410 420 430 440 450 460
1OG5-2C9A KRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASVPPFYQLCFIPV
_consrvd