Dear: I am trying to refine my model with loop refine protocol. But it is always said: ------------------------------------------------------------------------------------------------------- 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)
Here is my script, could you please give me some advices?
---------------------------------------------------------------------------------------- # 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 # 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