13 Apr
2010
13 Apr
'10
1:40 p.m.
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
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