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。