[modeller_usage] alignment of multiple templates

[Bo Yang <>]

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!

 

Bo

 

 

---

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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