Re: [modeller_usage] add restype to and how to select ligand

On 5/5/10 2:10 AM, Knut J Bjuland wrote: > If wish to use acetyl-coa in model which use a polypetid as template. > How can I specify to modeller to use the atom in hetatm since I often > get other petids if I cut of the amino acid to get better alignment.

If I understand you correctly, you have multiple ligands in the template but want only one in the model. That's straightforward - simply list all the ligands in the *template* sequence, but only the one you want in the *model* sequence. For example, if your template has three ligands, but you only want the last one in the model, your alignment should look like:

template: AAAAAAA...* model: BBBBBBB--.*

Ben Webb, Modeller Caretaker