建模脚本build_profile.py没有得到正确的输出

Question

9用于蛋白质结构建模，顺便说一下它在python2.3上运行，我以前安装过，当我运行脚本时输出不正确，它应该是所有蛋白质序列的对齐，y只得到第一个序列，没有别的，我应该为获得正确的输出做什么这是脚本

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')

，输出为

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

，输出应为

>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
AFKDADVALLVGARPRGPGMERKDLLEANAQIFTVQGKAIDAVASRNIKVLVVGNPANTNAYIAMKSAPSLPAKN
FTAMLRLDHNRALSQIAAKTGKPVSSIEKLFVWGNHSPTMYADYRYAQI--DGASVK--DMINDDWNRDTFLPTV
GKRGAAIIDARGVSSAASAANAAIDHIHDWVLGTA-GKWTTMGI--PSDGSYGIPEGVIFGFPVTTE-NGEYKIV
QGLSIDAFSQERINVTLNELLEEQN-GVQHL----*
..............

Answer 1

获得有关modeller问题答案的最佳位置是相关邮件列表:[e-mail].