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

 

> Date: Wed, 14 Apr 2010 14:24:15 -0700
> From: modeller-care@salilab.org
> To: knutjbj@hotmail.com
> CC: modeller_usage@salilab.org
> Subject: Re: [modeller_usage] model with ligand
>
> On 04/13/2010 11:37 PM, Knut J Bjuland wrote:
> > 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.
>
> In your alignment you have two sequences: the template and the model.
> The ligand you want to model needs to be in both sequences, of course,
> since Modeller builds the model sequence, and it needs to see the ligand
> in the template in order to know what the model ligand should look like.
> But your template sequence should contain *all* of the ligands that are
> in the template PDB file. Just align the model ligand with whichever one
> of the template ligands you want to use.
>
> For example, if your template PDB contains 4 HETATM residues after the
> amino acid chain, and you want to use only the second of these in your
> model, your alignment should look something like
>
> >P1;template
> structureX(etc.)
> YVINDS....*
>
> >P1;model
> sequence(etc.)
> YVINDS-.--*
>
> Alternatively, you can change the residue range in the template header
> (structureX line) to instruct Modeller to stop reading the PDB once it
> reaches a given ligand's residue number - then you don't need to list
> all the ligands in the sequence, just those up to that residue number.
> Or you can make a copy of the PDB file, and edit it in a text editor so
> that it only contains the ligands you're interested in.
>
> Ben Webb, Modeller Caretaker
> --
> modeller-care@salilab.org http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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