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. How do I instruct t saling to add the ligand. I have tried add env.io.hydrogen = True env.io.water = True env.io.hetatm=True
with out much success.
Knut J _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969
On 04/13/2010 01:03 AM, Knut J Bjuland wrote: > 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
Hi thanks
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.
Knut J
Den 13.04.2010 22:40, skrev Modeller Caretaker: > On 04/13/2010 01:03 AM, Knut J Bjuland wrote: >> 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
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
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 _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969
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
participants (2)
-
Knut J Bjuland -
Modeller Caretaker