Now that Coot uses the restraints dictionary to render ligands it has
become apparent that the method of doing so is problematic for typical
Say for example your read in
complex-XYZ00123456.pdb in which the ligand is called LIG
You read in the dictionary for XYZ00123456 and the ligand looks fine.
Now read in
complex-XYZ00123457.pdb in which the ligand is called LIG
Different compound, same name, so same dictionary is used to render
Result: tangled mess
Read in dictionary for XYZ00123457 and now complex-XYZ00123457 looks
fine but XYZ00123456 is a tangled mess because the restraints for LIG
have been overwritten.
So I am considering adding in a hack to Coot to make this situation less
A potential hack is to specify that it is to be used for molecule number
N (or a set of Ns) only.
Doing this would make Coot internals messy so I have make this request
for comments before I spend time reworking things and producing a
solution that no-one will use.