|
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: > To: > CC: > 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 > -- > http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage Hotmail: Trusted email with powerful SPAM protection. Sign up now. |