Re: [modeller_usage] model with ligand

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 04/15/2010 04:23 AM, Knut J Bjuland wrote:
> I use multiple sequence and one template pdb to get an improved
> alignment. I also just use part of the protein around the active domain.
> Should I also add the ... at all the other seqeunce as well as the one I
> am modelling.

Modeller can use multiple templates (structures) to model a single 
sequence (model) but not the other way round. Its alignment methods 
don't work with ligands anyway, so for alignments you should turn 
env.io.hetatm off and not use any '.' one-letter codes. Then add in '.' 
where necessary for the modeling step.

> Is there anything in particular I should keep in mine when
> using acetyl-coA when it is an ligand.

No, Modeller doesn't care about the type of the ligand, so you don't 
have to do anything special.

	Ben Webb, Modeller Caretaker
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