Modeller多序列建模简单教程

1.下载目的基因氨基酸序列，faste格式2.准备目的序列qseq1.ali文件，将faster格式文件修改为下列形式：P1;qseq1sequence:qseq1:::::::0.00:0.00MNKKTITKVFSILSSTAMLPILSSINVTADTVTTEGVKYEFEKGISNGAQIYTDYTGTTDDGLPIDLKGASCSFIGQKGTSTSVDINVDKAGLYELIVNYAEPFDKNKKVQYLNVNGTNQGEVSFPYSLGWKNLSAGIVKLNAGTNNIQFESYWGYTFFDYLIVKPADESITNLKGDKTLVNPNATNEAKALKSYLADVYGKHIISGQQELCGSHNYSGSESDFAYIKEKTGKMPALRGFDFMNYRGNGLLWDDNCAERVIDWYKNQNGIPTVCWHWFSPGNIGKKGDSSFYTKDTTFSISKALTPGTEENTAMMNDIELMAGKFKQLQDAGVPVLFRPLHEAEGGWFWWGAEGPENCVKLYRLLYDQFTNKYGLNNLIWVWTSYTYETSPQWYPGDDVVDIVGYDKYNAKDGKPNGSAISSTFYNLVQATGGKKLVTMSENDTIPQVSNLTNEMAGWLYFCPWYGYWLTGEQNNPVSWLNEIYNSDYCITLDELPNLKTYPISSTIDPKITYGDLNGDTKINAIDMALMKSYLLGNITEFKVPIAAADLDGNKSVNAIDLALLKKYLLGNLSIFPSNGK*修改名称，并加*，另存为qseq1.ali文件3.下载模板，blastp中搜索pdb数据库，选取前几位晶体解析基因，去PDB数据库下载.pdb文件，分别编号tseq1、tseq2、tseq3、tseq4。4.准备脚本：（1）复制下列文本至一新的写字板中#IllustratestheSALIGNmultiplestructure/sequencealignmentfrommodellerimport*log.verbose()env=environ()env.io.atom_files_directory='./:../atom_files/'aln=alignment(env)for(code,chain)in(('tseq1','A'),('tseq2','A'),('tseq3','A'),('tseq4','A')):mdl=model(env,file=code,model_segment=('FIRST:'+chain,'LAST:'+chain))aln.append_model(mdl,atom_files=code,align_codes=code+chain)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_cutoff=3.5,normalize_pp_scores=False,rr_file='$(LIB)/as1.sim.mat',overhang=30,gap_penalties_1d=(-450,-50),gap_penalties_3d=(0,3),gap_gap_score=0,gap_residue_score=0,dendrogram_file='fm00495.tree',alignment_type='tree',#If'progresive',thetreeisnot#computedandallstructueswillbe#alignedsequentiallytothefirstfeature_weights=weights,#Foramultiplesequencealignmentonly#thefirstfeatureneedstobenon-zeroimprove_alignment=True,fit=True,write_fit=write_fit,write_whole_pdb=whole,output='ALIGNMENTQUALITY')aln.write(file='fm00495.pap',alignment_format='PAP')aln.write(file='fm00495.ali',alignment_format='PIR')aln.salign(rms_cutoff=1.0,normalize_pp_scores=False,rr_file='$(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')修改上述几处为所选模板名称，另存为script2.py文件。（2）复制下列文本至一新的写字板中frommodellerimport*log.verbose()env=environ()env.libs.topology.read(file='$(LIB)/top_heav.lib')#Readalignedstructure(s):aln=alignment(env)aln.append(file='fm00495.ali',align_codes='all')aln_block=len(aln)#Readalignedsequence(s):aln.append(file='qseq1.ali',align_codes='qseq1')#Structuresensitivevariablegappenaltysequence-sequencealignment:aln.salign(output='',max_gap_length=20,gap_function=True,#tousestructure-dependentgappenaltyalignment_type='PAIRWISE',align_block=aln_block,feature_weights=(1.,0.,0.,0.,0.,0.),overhang=0,gap_penalties_1d=(-450,0),gap_penalties_2d=(0.35,1.2,0.9,1.2,0.6,8.6,1.2,0.,0.),similarity_flag=True)aln.write(file='qseq1-mult.ali',alignment_format='PIR')aln.write(file='qseq1-mult.pap',alignment_format='PAP')修改上面几处为目的基因名称，另存为script3.py文件。（3）复制下列文本至一新的写字板中frommodellerimport*frommodeller.automodelimport*env=environ()a=automodel(env,alnfile='qseq1-mult.ali',knowns=('tseq1A','tseq2A','tseq3A','tseq4A'),sequence='qseq1')a.starting_model=1a.ending_model=5a.make()修改上面几处为相应的名称，另存为script4.py文件。5.建模（1）将上述所有文件（目的基因qseq1.ali、模板.pdb文件、三个脚本文件script.py）复制至D：\Modeller\Modeller9.19bin\test文件夹中（D：\Modeller\Modeller9.19为文件安装位置，选择至自己的软件安装位置即可）（2）按照下列方法输入信息运行完成后该文件夹中出现5个生成的.pdb模型文件，即为构建好的模型。