Hi thanks
If I for instance wanted model myoogxyglobin based on hemoglobin which is polydimer. In my example I used chain A for my modeling how do I indicate for modeller to use just one ligand from the chain A.
Knut J
Den 13.04.2010 22:40, skrev Modeller Caretaker: > On 04/13/2010 01:03 AM, Knut J Bjuland wrote: >> I am useing modeller to do modell protein. There are some point that >> I do not get in adding the ligand. Is it possible to add the lign in >> the alignment witouth adding manual to the aln file. > > No, you need to add it manually. > >> How do I instruct t saling to add the ligand. > > You can't. SALIGN aligns protein sequences - its dynamic programming > residue-residue distance matrix does not include distances for ligands, > so it cannot align these sequences (it will treat them as gaps). Align > your protein sequences first, then manually add the ligand(s) to your > alignment. > > Ben Webb, Modeller Caretaker