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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http://www.salilab.org/modeller/
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