[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] Oligomer Modelling

Manjunatha Karpenahalli wrote:
I try to model homedimer with few point mutations using hometrimer as a template. In the alignment file I specified to use only chain A and chain B from the template, but the out put dimer model has different monomer-monomer interface than template. I used standard script( http://salilab.org/modeller/9v4/manual/node28.html) and the alignment file:

If this is your actual alignment file, then there are some problems with it:

1. The chain break character is a forward slash (/). You seem to be
   using a backward slash (\). That won't work.

2. You don't have anything aligned with your second chain, so Modeller
   will build a very poor model for that. What you have as your
   alignment is something like:

   aaaa/----   template 1
   bbbb/----   template 2
   XXXX/YYYY   model

   The result is that Modeller will use *both* of your templates to
   model the first chain, but will have no homology information at all
   for the second - so you'll essentially get an extended chain. If you
   really want to build a dimer using two single chain templates, your
   alignment should look something like:

   aaaa/----   template 1
   ----/bbbb   template 2
   XXXX/YYYY   model

   This, however, is still not ideal (see point 3).

3. You have split your template 1EFA into two single chain templates.
   Since Modeller has no way to tell that these two templates are
   actually from the same PDB, it can't build distance restraints
   between the two chains, and thus the interface will not be conserved.
   In order to conserve the interface, you should use a single dimer
   template rather than two monomer templates, i.e.

   aaaa/bbbb    template 1
   XXXX/YYYY    model

In your case, your alignment file would thus look like:

sequence:inv3HD:1:.: 331 ::MODELLING PROTEIN:undefined::
(sequence of A chain) / (sequence of B chain)

structureX:1EFA:2:A: 329 :B:LAC REPRESSOR:undefined::
(sequence of A chain) / (sequence of B chain)

Note that in the header for the 1EFA template you now tell Modeller to read from residue 2 in the A chain all the way through to residue 329 in the B chain. Look at the alignment file that goes with that script I pointed you to (twochain.ali, in examples/automodel/) for a working example. Notice that both the template and the model are dimers.

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage