On 29/11/2023 10:58, Subscribe COOT Marie M üller wrote:
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Dear all,
I am wondering if it is somehow possible to model two different amino acids in
the same position. We are working on a dataset from a mixed sample and we think
we obtained crystals that contain two sequences (they are very similar, 95%
identity). There are a few positions in which the sequence differs and the
electron density supports both sequence variants. I would like to model both
and then see if this improves the refinement or if one of them will be kicked
out again.
I was hoping I could approach this similarly to how we model alternative
conformations. So I edited the residue into conformation A with an occupancy of
0.5 and merged the other residue into the same structure (in conf B, occ 0.5).
However the residue will be renumbered automatically and added to the end of
the chain, if I try to renumber the residue to sit in the same position coot
will tell me:
WARNING::could not renumber residue range. Maybe your selection overlaps with existing residues. Please revise your selection.
Are you aware of any way to model two different residues in the same position
or will COOT always prevent this?
Dear Marie,
Coot does not deal well with this issue (micro-heterogeneity).
Coot does not allow the addition of micro-heterogeneity.
Coot can just about parse it and draw it, maybe even refine it, but many
modelling operations will fail.
I'd model the other conformer as a single residue an a new model
molecule (get the chain id and residue number and occupancy correct) and
then hand paste that residue into the file that contains the rest of
molecule. A very "meh" solution, I admit, but to handle
micro-heterogeneity across the board would take a year or so and there
are other things to do at the moment.
Regards,
Paul.
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