On 23/12/2022 16:48, Joshua Arribere wrote:
Hello,
I am trying to understand how to restore a chain after a deletion in
coot. I have deleted some residues (using delete-residue-range). The
residues are visually gone, and replaced with a dotted line (a loop)
between the flanking residues. I am not sure the best way to seal this
gap. I can link the flanking residues, so that they remain bound, but
two things make me think this is not the right way to go about it: (1)
the number of the residues still assumes there is a gap, even after
renumbering, and (2) the loop remains (of course, I could hide the
loop and solve the problem cosmetically, but I think the loop is
telling me that coot things the residues are still there).
Is linking the "right" way to do this? If so, how do I resolve the
numbering issue (by separately re-numbering the two halves?)?
Shouldn't the dotted line loop go away? Or is linking wrong?
I can find a lot in coot docs about mutating, deleting, but it seems
inserting is far less common.
I am unclear about the details of the situation. This is my guess: You
have deleted residues from a model that had residues where there were no
residues in you crystal. Now you want to anneal the gap. So simply
renumber the c-terminal fragment by an offset of negative few so that
there is no gap in the residue numbering. After you have done that, coot
will no longer draw a missing residues loop and may draw a peptide bond
between the two fragments. If that is the case, you can give it a quick
triple-refine to optimise the geometry over the newly-formed peptide. So
linking is not the right way to do it and I don't think that you want to
insert (that is, if I have understood the problem correctly).
Paul.
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