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Re: [modeller_usage] modeling an oligomer



Douglas Kojetin wrote:
I would like to create an oligomeric (hexamer) model. I have a Ca- only hexameric model (chains A-F) to use for the template and an experimentally determined monomer structure I would like to use for the target.

If you have a multimer template, and want to build a multimer model, that's straightforward. Just use the regular modeling scripts, and add chain breaks (/) in your alignment file accordingly. See http://www.salilab.org/modeller/9v4/manual/node28.html for an example. Your alignment would look like

>P1;hextemplate
structureX:hextemplate.pdb:1:A:4:F::::
aaaa/bbbb/cccc/dddd/eeee/ffff*
>P1;model
sequence:::::::::
AAAA/BBBB/CCCC/DDDD/EEEE/FFFF*

If you also want to use your monomer structure, just align it with one of the chains of the other template and build a model using both templates. In principle you could use 6 copies of your monomer structure, each aligned with a different chain, e.g.

>P1;hextemplate
structureX:hextemplate.pdb:1:A:4:F::::
aaaa/bbbb/cccc/dddd/eeee/ffff*
>P1;expmtmonomer1
structureX:expmtmonomer.pdb:1:A:4:A::::
aaaa/----/----/----/----/----*
>P1;expmtmonomer2
structureX:expmtmonomer.pdb:1:A:4:A::::
----/bbbb/----/----/----/----*
etc.
>P1;model
sequence:::::::::
AAAA/BBBB/CCCC/DDDD/EEEE/FFFF*


You could also build a monomer model (aligned to just one chain of your template - just change the sequence for the model, leaving the templates unchanged, and replace all but one chain with gaps) but then you have to figure out how to fit your 6 monomer models together after modeling. That sort of protein-protein docking is outside the scope of the Modeller package.

I've attempted to do this using the "model-myini.py" script as described here:

No, don't do that. That just sets the starting point for the optimization - not the final structure - and so is only useful in cases where the optimizer needs a 'helping hand' to build the model (for example, you may manually correct serious problems, such as knots in the protein chain, that the optimizer wouldn't be able to fix itself). If you want to influence the *final* structure, include it as a template.

	Ben Webb, Modeller Caretaker
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