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  • 利用多个模版来构建同源模型

    首先生成ali文件,其中包含多个模版的序列:

    C; A multiple alignment in the PIR format; used in tutorial
    
    >P1;5fd1
    structureX:5fd1:1    :A:106  :A:ferredoxin:Azotobacter vinelandii: 1.90: 0.19
    AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
    EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*
    
    >P1;1bqx
    structureN:1bqx:   1 :A: 77  :A:ferredoxin:Bacillus schlegelii:-1.00:-1.00
    AYVITEPCIGTKCASCVEVCPVDCIHEGEDQYYIDPDVCIDCGACEAVCPVSAIYHEDFVPEEWKSYIQKNRDFF
    KK-----------------------------*
    
    >P1;1fdx
    sequence:1fdx:1    : :54   : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
    AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED-----------------
    -------------------------------*
    
    # Homology modeling with multiple templates
    from modeller import *              # Load standard Modeller classes
    from modeller.automodel import *    # Load the automodel class
    
    log.verbose()    # request verbose output
    env = environ()  # create a new MODELLER environment to build this model in
    
    # directories for input atom files
    env.io.atom_files_directory = ['.', '../atom_files']
    
    a = automodel(env,
                  alnfile  = 'align-multiple.ali', # alignment filename
                  knowns   = ('5fd1', '1bqx'),     # codes of the templates
                  sequence = '1fdx')               # code of the target
    a.starting_model= 1                 # index of the first model
    a.ending_model  = 1                 # index of the last model
                                        # (determines how many models to calculate)
    a.make()                            # do the actual homology modeling
    


     其实步骤很简单,只需要在knowns中用列表的形式指定多个模版即可。

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  • 原文地址:https://www.cnblogs.com/dyllove98/p/3172421.html
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