Dear Marie, look at crambin (pdbcode 1EJG).
In the past (might have changed) this crashed Coot when loading the
structure until you add*
allow_duplicate_sequence_numbers()
to $HOME/.coot.py in OSX or the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
directory for configuration - these can be found (added to) the
directory in which Coot was installed (e.g. C:\WinCoot).
For naming the residues correctly so it behaves fine during refinement
(in phenix) look at
https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12
example 5
Br, Georg.
Am 29.11.2023 um 11:58 schrieb Subscribe COOT Marie M üller:
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?
Best,
Marie Müller
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