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 refiningThe 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 *

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): # 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

m.make()

or should I try both?

Thanks:) 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 >

Hello Ben thank you for your kind update:).

I tired the ModLoop, however, have 91 residues accordingly was rejected due to length. If there is way to work around this error let me know please, thanks:)

My Enter Loop Segment promoting this error.

88:A:100:A: 88:B:100:B: 88:C:100:C: 88:D:100:D: 88:E:100:E: 88:F:100:F: 88:G:100:G:

(I will continue with the other Advanced Tutorial.)

Best, Joel

On Thu, Sep 22, 2022 at 8:54 PM Modeller Caretaker < modeller-care@salilab.org> wrote:

> On 9/22/22 9:57 AM, Joel Subach wrote: > > In my case which tutorial should I follow for this loop refinement: > > The advanced tutorial at > https://salilab.org/modeller/tutorial/advanced.html is the best place to > start. The Cryo-EM tutorial scores the resulting loop models based on > their fits into a cryo-EM map, so wouldn't make sense for you unless you > also have such a map. > > Alternatively, you can use the ModLoop web server at > https://modbase.compbio.ucsf.edu/modloop/ > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >