One of the problems - perhaps the major one - is that you have two
residues that have the same residue number and chain-id.
So, one of them needs to be changed (to residue 2, say).
I don't think it is the problem. In the main chain I have LLP and LYS
both with the same chain-id and res number and coot has no problem with
them.
Secondly, you have differing alt confs and that is a signal to Coot (at
least) that these residues don't interact - so a PPE-GLU link (if that
is what you are after) will never be made - nor will any non-bonded
interactions.
I'm not looking for the PPE-GLU interactions (actually PPE contains GLU
moiety). What I'm trying to visualise is combination of three active
site components of which free GLU is one of the alternatives.
Thirdly, when Coot tried to make restraints it gives you a "dictionary
problem?" warning - whereas in this case, it is due to an atom selection
problem (no atoms selected).
No, there is no 'directory problem' reported. I'm away from my
workstation hence cannot reproduce the error exactly but it is related
to missing restraints and reading cif file.
Andrzej
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