Modeller多序列建模简单教程

精品文档 1欢迎下载 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 qseq1 sequence qseq1 0 00 0 00 MNKKTITKVFSILSSTAMLPILSSINVTADTVTTEGVKYEFEKGISNGAQIYTDYTGTTDDGLPIDLKGA SCSFIGQKGTSTSVDINVDKAGLYELIVNYAEPFDKNKKVQYLNVNGTNQGEVSFPYSLGWKNLSAGIVK LNAGTNNIQFESYWGYTFFDYLIVKPADESITNLKGDKTLVNPNATNEAKALKSYLADVYGKHIISGQQE LCGSHNYSGSESDFAYIKEKTGKMPALRGFDFMNYRGNGLLWDDNCAERVIDWYKNQNGIPTVCWHWFSP GNIGKKGDSSFYTKDTTFSISKALTPGTEENTAMMNDIELMAGKFKQLQDAGVPVLFRPLHEAEGGWFWW GAEGPENCVKLYRLLYDQFTNKYGLNNLIWVWTSYTYETSPQWYPGDDVVDIVGYDKYNAKDGKPNGSAI SSTFYNLVQATGGKKLVTMSENDTIPQVSNLTNEMAGWLYFCPWYGYWLTGEQNNPVSWLNEIYNSDYCI TLDELPNLKTYPISSTIDPKITYGDLNGDTKINAIDMALMKSYLLGNITEFKVPIAAADLDGNKSVNAID LALLKKYLLGNLSIFPSNGK 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 Illustrates the SALIGN multiple structure sequence alignment from modeller import log verbose env environ env io atom files directory atom files 精品文档 2欢迎下载 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 the tree is not computed and all structues will be aligned sequentially to the first 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 fm00495 pap alignment format PAP aln write file fm00495 ali alignment format PIR 精品文档 3欢迎下载 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 from modeller import log verbose env environ env libs topology read file LIB top heav lib Read aligned structure s aln alignment env aln append file fm00495 ali align codes all aln block len aln Read aligned sequence s aln append file qseq1 ali align codes qseq1 精品文档 4欢迎下载 Structure sensitive variable gap penalty sequence sequence alignment aln salign output max gap length 20 gap function True to use structure dependent gap penalty alignment 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 from modeller import from modeller automodel import env environ a automodel env alnfile qseq1 mult ali knowns tseq1A tseq2A tseq3A tseq4A sequence qseq1 a starting model 1 a ending model 5 a 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 精品文档 5欢迎下载 复制至 D Modeller Modeller9 19 bin test 文件夹中