Quentin Vicens wrote:
> Hi folks,
Hi Quentin,
> I am using Coot 0.4.1 and CNS 1.1 in order to refine a series of single mutants (substitution,
> deletion or insertion) that we solved by MR using the structure of the wild type.
>
> The problem we have is that when removing a residue, Coot does not connect the remaining
> residues back together. For example, if we remove residue 450, then we have a break between the
> remaining residues 449 and 451 (even after having moved them so they would be within bonding
> distance). I ran the PDB into generate_easy on CNS after having removed the O3’ (of residue 449)
> and the 5’-phosphate (of residue 451). Generate_easy rebuilt those and they appear connected in
> Pymol, but still not in Coot.
Sad to say, Coot doesn't do what you want (it should do, and will do).
Coot will indeed not try to bond things that do not have continuous
numbering.
> So I am kind of stuck as then I can’t use the real-space refinement functions of coot to modify
> that zone, and I am not sure how CNS will treat that region during refinement anyway.
Indeed. I suspect that by default it would treat it as Coot does (i.e.
unbonded).
> A colleague
> told me I would have to renumber the residues so that the numbering would be continuous, but I
> wish to avoid that since it would make our forthcoming comparison of these mutants impossible.
I suppose that you could renumber to refine/anneal the break and then
reverse the renumbering afterwards? Tedious. You can use the scripting
function renumber-residue-range to make it less so.
Paul.
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