Re: [modeller_usage] Including ligand from template

On 4/15/14, 2:05 AM, James Starlight wrote: > I've followed 1st modeller tutorial making alignment of my target > against 1 template (with the inclusion of hetatm from the template). As > the result I've obtained the below alignment

As pointed out already, you haven't told Modeller to put the ligand in the model. Is it possible that you modified the 2rh1.pdb file? Your template sequence doesn't match the one in 2rh1 from PDB (there's an extra sequence in the official PDB from residue 1002:A to 1161:A that isn't in yours). Maybe you removed the ligand by mistake too.

Ben Webb, Modeller Caretaker