Hello Ben thank you for your kind update: ). In my case which tutorial should I follow for this loop refinement: 1. ) Modeling with cryo-EM Step 7: Refine models with loop modeling or, 2. ) Loop refining The loop optimization method relies on
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Hello Ben thank you for your kind update:).

In my case which tutorial should I follow for this loop refinement:


Modeling with cryo-EM

Step 7: Refine models with loop modeling



Loop refining

The loop optimization method relies on a scoring function and optimization schedule adapted for loop modeling. It is used automatically to refine comparative models if you use the LoopModel class rather than AutoModel; see the example below.
# Loop refinement of an existing model
from modeller import *
from modeller.automodel import *

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:A', '283:A'))

m = MyLoop(env,
           inimodel='TvLDH-mult.pdb', # initial model of the target
           sequence='TvLDH')          # code of the target

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

 or should I try both?

Joel 🚀

On Wed, Sep 21, 2022 at 12:09 AM Modeller Caretaker <modeller-care@salilab.org> wrote:
On 9/20/22 8:52 AM, Joel Subach via modeller_usage wrote:
> Hi, I loop missing residue MODELLER modeled a heptamer both
> unrestrained and restrained with the former exhibiting an RMSD
> of 0.295 while the restrained exhibited an RMSD of 0.0.
> The restrained model´s missing residue loops, however, are too
> dynamic and seem to be broken when visualized via Pymol.
> Accordingly, is there a way to generate the restrained version to
> exhibit intact loops so that I may keep this version because of its
> 0.0 RMSD?

When you have regions like this that are not aligned with a template,
the only restraints on them in standard comparative modeling are from
the CHARMM forcefield. This will attempt to generate sensible
stereochemistry, but if you want more native-looking loops, you'll want
to refine them using the loop modeling protocol. You have long loops
though - you'll definitely need to build at least several hundred loop
models. If they still look too constrained, you might consider
broadening the residue range in your selection to include a few residues
either side of the loop.

        Ben Webb, Modeller Caretaker
modeller-care@salilab.org             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage