[Chimera-users] Modeller missing residues

[Danilo Boškovic]

Dear all,

I have just made a model according to the tutorial for missing residues 
for Modeller. I wanted all atoms not to move so i used the script at the 
bottom of the tutorial. It seems to work but when i do match align i can 
still see a very very slight misalignment in certain areas that are not 
supposed to be touched. I used residue ranges from the alignment window 
by just clicking on residues and reading their positions at the bottom 
of the alignment window (might be an issue with numbering?). As a 
starting structure i used the structure i wanted to take the loops from 
and as a template structure i used the structure in which i wanted to 
fill the loops (100% same, difference is in states). I edited the script 
in chimera as follows:

from modeller import *
from modeller.automodel import *

namelist = open( 'namelist.dat', 'r' ).read().split('\n')
tarSeq = namelist[0]
template = tuple( [ x.strip() for x in namelist[1:] if x != '' ] )

log.verbose()

env = environ()

env.io.atom_files_directory = ['.', './template_struc']

class MyModel(automodel):
		def select_atoms(self):
                     return selection(self.residue_range('312', '315'),
                     self.residue_range('630', '642'),
                     self.residue_range('668', '674'))
		#code overrides the special_restraints method

		#def special_restraints(self, aln):

		#code overrides the special_patches method.
		# e.g. to include the addtional disulfides.
		#def special_patches(self, aln):

a = MyModel(env, sequence = tarSeq,
		# alignment file with template codes and target sequence
		alnfile = 'alignment.ali',
		# PDB codes of the templates
		knowns = template)

a.starting_model = 1
a.ending_model = 1
loopRefinement = False

a.assess_methods = (assess.GA341, assess.normalized_dope)

a.make()

Link to tutorial:
https://salilab.org/modeller/wiki/Missing%20residues