Dear:
I am trying to refine my model with loop refine protocol. But it is always said:
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File "/usr/lib64/python2.4/site-packages/modeller/coordinates.py", line 226, in __getitem__
(self.offset, self.length, self.suffix))
File "/usr/lib64/python2.4/site-packages/modeller/util/modutil.py", line 19, in handle_seq_indx
int_indx = lookup_func(*args)
File "/usr/lib64/python2.4/site-packages/modeller/coordinates.py", line 289, in _indxres
raise KeyError("No such residue: %s" % indx)
KeyError: 'No such residue: 273:'
Here is my script, could you please give me some advices?
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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):
# One loop from residue 19 to 28 inclusive
return selection(self.residue_range('273', '283'))
#return selection(self.residue_range('1:', '4:'))
m = MyLoop(env,
inimodel='input.pdb', # initial model of the target
sequence='model') # code of the target
m.loop.starting_model= 0 &nbs
p; # index of the first loop model
m.loop.ending_model = 100 # index of the last loop model
m.loop.md_level = refine.very_fast # loop refinement method
m.make()
KeyError: 'No such residue: 206:'