Hi folks,
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.
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. 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 would welcome anybody's suggestion!
Thanks,
Quentin
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