On 14/01/15 16:04, Sampson, Jared wrote:
> Along the same lines as Dialing’s recent post about inserting a
> residue, I’d like to ask: Is it possible to insert a residue with an
> insertion code in the residue number? For example, what’s the best
> way to insert residue 100A between residues 100 and 101?
No. Sorry. Coot is pretty unsophisticated about insertion codes.
>
> This situation arises frequently for me in antibody CDR loops, for
> example. I ran into it most recently just last week, and Coot
> wouldn’t allow this kind of insertion, even though the consecutively
> numbered residues were too far apart to be covalently linked. (In the
> terminal window, it explained "that residue was not at a terminus.”)
> My workaround has been either to increment the residue numbers of the
> C-terminal portion of the chain, then renumber manually in a text
> editor; or, to position a lone amino acid in approximately the right
> spot, save the coordinates, copy them manually into the working PDB
> and adjust the numbering in a text editor, reload the PDB in Coot, and
> real space refine the loop with the insertion.
That's disgusting. Well done :-)
I'd copy the C-terminal fragment //A/101-102, say (making mol2)
Then delete //A/101-102 from the current model,
Then add new molecule to add a C-terminal residue at (what will
initially be) 101 "". Then juggle the insertion code and residue number
with change_residue_number()
Then replace fragment from mol2 into the current molecule.
Might work.
Paul.
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