my current project involves the refinement of an tertrameric
protein, which is already an homology model generated with modeller.
Now, I tried to refine the existing model, because its N-terminus
should be alpha helical.My strategy involved creating an alpha-helix
and generating a new chimeric protein with this.
That should work, since Modeller builds models that look like the
templates - it doesn't matter where the templates come from.
In a second step I created a pir file, which seems to cause the
problems. I followed the Pir-format on the modeller webpage, but the
python script exits pointig at problems in the pir file.
Clearly you will need to fix this problem before you can proceed. If you
can't figure out what the problem is with the Modeller log file in front
of you (it usually gives you a pretty clear indication what the problem
is) then it's unlikely anybody can help you *without* seeing that log
file! If you can't figure it out, tell us what the error is.
Your Python script looks fine. Your alignment also looks OK, but note
that your sequence is aligned both with your alpha-helical protein and
the 'My-PDB' template. So Modeller will try to build a model which looks
like *both* proteins. That's not going to work, since they have
different secondary structures - align it with one or the other.
As Anthony points out, you can skip the intermediate step of producing
an alpha-helical template and just include the alpha-helical restraints.
The same consideration applies though - you will need to modify your
alignment in this region so that your model does not align with My-PDB,
otherwise the alpha-helical restraints will likely conflict with its
secondary structure.
I don't know, how to
create four helices or assign the already created to all four monomers.
If you mean you have this same helix in all four monomers, then you
would need to add three more copies of the alpha-helical template
aligned with each of the chains (so you'd have 5 templates in all).
Anthony's solution would be cleaner here though.