一：对生成的模型的所有的loop区域进行优化
# Homology modeling by the automodel class
from modeller import *
from modeller.automodel import * # Load the automodel class
log.verbose()
env = environ()
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
a = loopmodel(env,
alnfile = 'alignment.ali', # alignment filename
knowns = '5fd1', # 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.md_level = None # No refinement of model
a.loop.starting_model = 1 # First loop model
a.loop.ending_model = 4 # Last loop model
a.loop.md_level = refine.fast # Loop model refinement level
a.make() # do homology modeling
a.loop.starting_model 和 a.loop.ending_model用于指定产生优化loop后的模型数量。
二：指定要优化的loop区域
from modeller import *
from modeller.automodel import *
log.verbose()
env = environ()
env.io.atom_files_directory = ['.', '../atom_files']
# Create a new class based on 'loopmodel' so that we can redefine
# select_loop_atoms
class MyLoop(loopmodel):
# This routine picks the residues to be refined by loop modeling
def select_loop_atoms(self):
# Two residue ranges (both will be refined simultaneously)
return selection(self.residue_range('19:', '28:'),
self.residue_range('45:', '50:'))
a = MyLoop(env,
alnfile = 'alignment.ali', # alignment filename
knowns = '5fd1', # codes of the templates
sequence = '1fdx', # code of the target
loop_assess_methods=assess.DOPE) # assess each loop with DOPE
a.starting_model= 1 # index of the first model
a.ending_model = 1 # index of the last model
a.loop.starting_model = 1 # First loop model
a.loop.ending_model = 2 # Last loop model
a.make() # do modeling and loop refinement
这个过程需要自己定义一个Myloop类，这个类继承了loopmodel类，这个类要重写loopmodel类中的select_loop_atoms()方法。