Re: [modeller_usage] Modelling in/dels and residue substitutions

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 11/11/19 1:55 PM, Jared Slosberg wrote:
> I am interested in creating models for variants of a protein with a 
> known cryo-EM structure. My approach for the substitutions is to use 
> the mutate_model script. However, I would also like to model predicted 
> changes in structure to nearby residues. I altered the script in this 
> way in an attempt to optimize over a range of residues, but I saw no 
> difference in the resulting model than with only the one residue selected.
>
> modelname, respos, restyp, chain, start, stop, = sys.argv[1:]
>
> ...
>
> s = 
> selection(mdl1.chains[chain].residues[start],mdl1.chains[chain].residues[stop])

This will select the start residue and the stop residue, not the 
residues in between, which is probably not what you meant to do. 
residue_range() is probably what you want here:
https://salilab.org/modeller/9.23/manual/node174.html

That being said, I would probably just do regular comparative modeling 
in this case and fix any residue ranges you don't want to move:
https://salilab.org/modeller/9.23/manual/node23.html

> However, this has obviously left the ends of the aligned sections fixed 
> in space, so that the region that I want to fold "freely" is fixed at 
> these two points. This results in them "stretching out" rather than 
> being able to fold as I would like. I hope that I am being clear. Is 
> there better method to create variants with insertions that is more 
> flexible?

If you don't want the ends fixed, unalign a longer segment. If you do 
want them fixed but want better conformational sampling, this is 
precisely what loop modeling is designed for:
https://salilab.org/modeller/9.23/manual/node33.html

	Ben Webb, Modeller Caretaker
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