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。