On 1/3/22 7:50 AM, Samdani A wrote: > I am trying to model an ion, water and ligand from a template and below > is my alignment file. ...> The modelled structure generated without any error containing ion and > water. But only two atoms were observed in the modelled structure but > the ligand in the template contains 38 atoms. The atoms in ligand were > not retained in the model from the template.
I would need to see your PDB file to be sure, but Modeller copies ligand atoms from templates based on their names, so if multiple atoms have the same name, you will only get one atom in the output file. This can sometimes happen if your input PDB file is not in the correct format, e.g. you have the atom names in the wrong columns in the file.
Ben Webb, Modeller Caretaker