Modeller script build_profile.py doesnt get the correct output

9 for protein structure modelling, by the way it runs on python2.3, i made the installation previously, when i run the script the output isnt rigth it should be an aligment of all the protein sequences and y only get the fist sequence and nothing else what i should do for get the correct output this is the script

from modeller import*

log.verbose()
env = environ()

sdb = sequence_db(env)
sdb.read(seq_database_file='pdb_95.pir', seq_database_format='PIR',
     chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True)

sdb.write(seq_database_file='pdb_95.bin', seq_database_format='BINARY',
      chains_list='ALL')

sdb.read(seq_database_file='pdb_95.bin', seq_database_format='BINARY',
     chains_list='ALL')

aln = alignment(env)
aln.append(file='Brn3a.ali', alignment_format='PIR', align_codes='ALL')

prf = aln.to_profile()

prf.build(sdb, matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat',
      gap_penalties_1d=(-500, -50), n_prof_iterations=1,
      check_profile=False, max_aln_evalue=0.01)

prf.write(file='build_profile.prf', profile_format='TEXT')

aln = prf.to_alignment()

aln.write(file='build_profile.ali', alignment_format='PIR')

and the output is

>P1;Bra
sequence:Brn3a:    0: :    0: :::-1.00:-1.00
MMSMNSKQPHFAMHPTLPEHKYPSLHSSSEAIRRACLPTPPLQSNLFASLDETLLARAEALAAVDIAVSQGKSHP
FKPDATYHTMNSVPCTSTSTVPLAHHHHHHHHHQALEPGDLLDHISSPSLALMAGAGGAGAAAGGGGAHDGPGGG
GGPGGGGGPGGGPGGGGGGGPGGGGGGPGGGLLGGSAHPHPHMHSLGHLSHPAAAAAMNMPSGLPHPGLVAAAAH
HGAAAAAAAAAAGQVAAASAAAAVVGAAGLASICDSDTDPRELEAFAERFKQRRIKLGVTQADVGSALANLKIPG
VGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEGAQREKMNKPELFNGGEKKRKRTSIAAPEKRSLEAYFA
VQPRPSSEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFSATY*

and the output should be

>P1;Bra
sequence:Brn3a:    0: :    0: :::-1.00:-1.00
MMSMNSKQPHFAMHPTLPEHKYPSLHSSSEAIRRACLPTPPLQSNLFASLDETLLARAEALAAVDIAVSQGKSHP
FKPDATYHTMNSVPCTSTSTVPLAHHHHHHHHHQALEPGDLLDHISSPSLALMAGAGGAGAAAGGGGAHDGPGGG
GGPGGGGGPGGGPGGGGGGGPGGGGGGPGGGLLGGSAHPHPHMHSLGHLSHPAAAAAMNMPSGLPHPGLVAAAAH
HGAAAAAAAAAAGQVAAASAAAAVVGAAGLASICDSDTDPRELEAFAERFKQRRIKLGVTQADVGSALANLKIPG
VGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAEGAQREKMNKPELFNGGEKKRKRTSIAAPEKRSLEAYFA
VQPRPSSEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKFSATY*

>P1;1a5z
structure:1a5z:   63: :  229: :::-1.00:-1.00
--------------------------------------------------------------------------A
DLKGSDVVIVAAGVPQKPGETRLQLLGRNARVMKEIARNVSKYAPDSI-VIVVTNPVDV-LTYFFLKESGMDPRK
FGSGTVLDTARLRTLIAQHCGFSPRSVH-VYVIGEHGDSEV-PVWSGAMIGGIPLQNMCQVCQDSKILENFAEKT
KRAAYEIIERKGATHYA----------------------------------------------------------
-----------------------------------*

>P1;1b8pA
structure:1b8pA:    6: :  325: :::-1.00:-1.00
------VAVTGAAGQICYSLLFRIANGDMLGDQPVILQLLEIPKAQKALQGVMMEIDDCAFPLLAGMTAHADPMT
AFKDADVAL开发者_运维百科LVGARPRGPGMERKDLLEANAQIFTVQGKAIDAVASRNIKVLVVGNPANTNAYIAMKSAPSLPAKN
FTAMLRLDHNRALSQIAAKTGKPVSSIEKLFVWGNHSPTMYADYRYAQI--DGASVK--DMINDDWNRDTFLPTV
GKRGAAIIDARGVSSAASAANAAIDHIHDWVLGTA-GKWTTMGI--PSDGSYGIPEGVIFGFPVTTE-NGEYKIV
QGLSIDAFSQERINVTLNELLEEQN-GVQHL----*

..............

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