Re: [modeller_usage] ligand is not generated

On 5/12/21 6:18 PM, MARIANA BRANDI MENDONÇA PINHEIRO wrote: > I am having a problem with ligand generation. ... > The ligand is chain X at 2q3z = /.P.LPF./ > The models are created but without chain B/X or any ligand/polypeptide.

In order for the ligand to appear in the model, you must also include the '.' residue in your target (the 'sequence' entry in the alignment, P21980 in your case) and align it with the ligand in one of the templates. See also the example alignment align-ligand.ali at https://salilab.org/modeller/10.1/manual/node18.html

Ben Webb, Modeller Caretaker