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