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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
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loop_refine.py
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# 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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