Modelling in/dels and residue substitutions
Hello,
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])
Could you tell me if this change to the script would be expected to alter the resulting model, or if there is a better approach?
As well, my approach to modelling deletions is to create a manual alignment in which the residues around the deletion are unaligned from the template, so that they fold freely, and choosing the model [ generated with model_single.py ] with the lowest DOPE score if inspection looks good. [Here, GFF deleted].
one segment of query: FNSSAFFFSVV---------FL
aligned segment of template: FNSSA------FFFSGFFVVFL
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?
Thank you for your time,
Jared
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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Jared Slosberg -
Modeller Caretaker