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

[Modeller Caretaker <modeller-care@salilab.org>]

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
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage