Re: [modeller_usage] Modelling loop region in homodimer

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 11/10/2014 12:20 AM, aneesh cna wrote:
> I am a new comer to modeller. I am trying to model a ~15AA long missing
> loop region in a homo-dimer. Both  monomer units in the homo-dimer
> missing the loop region. Unfortunately, my template is a monomer unit.
> How can I model the loop region in both monomer together.?

Modeling the two loops is simple - just select both regions in 
select_loop_atoms() as shown at
http://salilab.org/modeller/9.14/manual/node36.html
But 30 residues is really long - you'll need to build a lot of models to 
hope to reasonably sample conformations.

Actually building the comparative model of a dimer from a monomer 
template is a different story, but this is already discussed at
http://salilab.org/modeller/9.14/manual/node29.html

	Ben Webb, Modeller Caretaker
--
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