Question

9对于蛋白质结构建模，顺便说一下它在python2.3上运行，我之前进行了安装，当我运行脚本时输出不严格它应该是所有蛋白质序列的一个对齐而且只能得到拳头序列，没有别的我应该做什么来获得正确的输出这是脚本

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

>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

有关modeller问题的最佳答案是相关的邮件列表：modeller_usage@salilab.org。

Modeller脚本build_profile.py没有得到正确的输出

1 个答案: