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Modeller---对蛋白指定的loop区域进行优化

已有 3948 次阅读 2013-9-23 20:13 |系统分类:科研笔记

背景:同源模建得到的loop区域不合理的时候,可以进行优化。

method:loop_refine.py

input:TvLDH.B99990001.pdb

需要refine的氨基酸:273-283

评价标准:DOPE


---------------------------------------------------------------------

loop_refine.py

--------------------------------------------------------------------

# Loop refinement of an existing model
from modeller import *
from modeller.automodel import *

log.verbose()
env = environ()

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

# Create a new class based on 'loopmodel' so that we can redefine
# select_loop_atoms (necessary)
class MyLoop(loopmodel):
   # This routine picks the residues to be refined by loop modeling
   def select_loop_atoms(self):
       # 10 residue insertion
       return selection(self.residue_range('273', '283'))

m = MyLoop(env,
          inimodel='TvLDH.B99990001.pdb', # initial model of the target
          sequence='TvLDHs')          # the name of output files prefix

m.loop.starting_model= 1           # index of the first loop model
m.loop.ending_model  = 10          # index of the last loop model
m.loop.md_level = refine.very_fast # loop refinement method; this yields
                                  # models quickly but of low quality;
                                  # use refine.slow for better models

m.make()



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