On 21/09/2023 18:58, Paul Emsley wrote:
On 21/09/2023 18:05, Kelvin Lau wrote:
Dear all
I am having trouble with an unnatural ligand/amino acid.
I have a structure very similar to PDB 6Q6H, 7TQR. They all have an
MDO residue that replaces three residues in a series G-A-S-G-D to
become G-MDO-D. MDO is in the Coot library.
I have been very used to replacing cysteines with CME with
Modelling>Replace residue. It works great, removes the OXT and all
the other atoms, can use real space refine directly.
For this MDO residue I find that it correctly fetches from the
dictionary, however, I cannot refine it. Whenever I click on an atom
and drag it just blows up or the atom gets stuck.
I have now opened up 6Q6H and 7TQR and tried to just refine the built
in MDO in those PDB, same thing happens.
Does anyone have any ideas of what might be going on? Also in general
for modified residues/unnaturals.
If you tell Coot that the group is a non-polymer it will believe you.
Use the Restraints editor to change the group to "peptide" (not tested).
Reply in haste ... repent at midnight.
This is old-fashioned advice it turns out (thanks to Garib).
Now that I come to actually look at one of the MDO beasties, it's not as
much like a peptide as I expected it to be, and so describing it as such
will induce Coot to throw itself to the floor in raging fit of geometric
conniptions.
As mentioned before, the CCP4 Monomer library has undergo a substantial
reworking/extension of the linking restraints.Concomitantly, Coot is now
fully capable of using the spangly new MDO-pept link description
completely automatically. It is an eyebrow-raising/forehead-wrinkling
concern that it didn't work this way for you.
Regards,
Paul.
FWIW, my Internal Chemist (and also the link restraints) tells me that
A141 H in 7tqr is pointing in the wrong direction.
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