用MODELLER构建好模型后对loop区域进行自动的优化过程

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。