Re: [modeller_usage] orientation of domains in chimera

[Modeller Caretaker <>]

Lillian chong wrote:
> I have two questions about using Modeller to build a chimera protein 
> based on two known structures (as in #1 of the FAQ):
> 1.  How does Modeller determine the initial relative orientations of the 
> two structures? 

The initial structure is the target sequence threaded onto the 
template(s) backbone, so the initial relative orientation will be 
essentially that of your input PDB files.

> 2.  Is there a way to extensively sample the relative orientations of 
> the two structures?  Perhaps through randomization of dihedral angles, 
> loop modeling, or some other approach?

Since you have no domain-domain restraints, Modeller will not be able to 
do a good job of optimizing the structure. So you should impose some 
sort of orientation restraint (maybe an angle between the mass centers 
of the two domains and a central point). Then you could perhaps vary 
that angle and build models to sample the orientation, but there are 
many ways to do this.

	Ben Webb, Modeller Caretaker
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