Hi Isabel thank you for your inquiry, if you restrain certain residues they should not move, maybe double-check to be sure
that you properly coded these residues to be restrained, thanks 🚀

On Mon, Oct 16, 2023 at 5:15 PM Isabel Elliott via modeller_usage <modeller_usage@salilab.org> wrote:

Good afternoon,


I am trying to model missing residues into my crystal structure following the method on the website: https://salilab.org/modeller/wiki/Missing_residues. I am also trying to restrain the crystal coordinates so that only missing residues move (and the rest of the original crystal coordinates remain the same) during refinement using the select_atoms method. However when I compare my final models produced by my script to my original crystal structure, I find that the side chains of several amino acids three of four amino acids away from the missing residues have been flipped. How can I ensure that only the missing residues are refined and the crystal coordinates remain the same? I am wondering if I’ve missed something important out of my script. See my script below.


Many thanks.


from modeller import *                      # Load standard Modeller classes

from modeller.automodel import *           # Load the AutoModel class


log.verbose()                              # Create log file 

env = Environ()


# directories for input atom files

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


env.io.water = True


# Only refine/move missing residues - restrain crystal coordinates

class MyModel(LoopModel):

        #picks residues to be refined by loop modelling

    def select_loop_atoms(self):

        #refines residue ranges defined simultaneously

        return Selection(self.residue_range('5:A', '13:A'),

                         self.residue_range('99:B', '105:B'),

                         self.residue_range('251:D', '256:D'))

# redefine the special_patches routine to include additional disulfides

    def special_patches(self,aln):




a = MyModel(env, alnfile = 'alignment.ali',            # alignment file

              knowns = 'xxx',                         # aa sequence of original template - crystal coordinates

              sequence = 'xxx_fill',                  # aa sequence of original template with missing residues filled in

              loop_assess_methods = (assess.DOPE,




a.starting_model= 1             # Index of the first model

a.ending_model  = 1             # Index of the last model


a.loop.starting_model = 1       # First loop refined model

a.loop.ending_model = 10        # Last loop refined model

a.loop.md_level = refine.fast   # Loop model refinement level


a.make()                        # Do modelling



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