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.
