See issue https://github.com/salilab/imp/issues/255. There was (and to some extent is) a lot of ambiguity about how setting individual coordinates to be optimized interactions with telling MC to move them.

On Tue, Sep 24, 2013 at 7:24 AM, Davide Baù <davide.bau@gmail.com> wrote:

Hi all,

I have a question about the "set_coordinates_are_optimized" function in IMP 2.0.1.

In the IMP versions < 2.0, to set the coordinates of a given particle, e.g., P1 to (0,0,0), I would use the following code:

> fixedP = "1"
> p = ps.get_particle(index)
> p.set_name(pname)
> if pname == fixedP:
> d = IMP.core.XYZ(p)
> d.set_coordinates(IMP.algebra.Vector3D(0,0,0))
> d.set_coordinates_are_optimized(False)

In IMP 2.0.1, even though, at this point, the coordinates of the particle "fixedP" are set to (0,0,0), the "set_coordinates_are_optimized" does not seem to work anymore (the coordinates of "fixedP" change during the optimization). Has this function beed replaced with a new one in the latest IMP version?

Thanks,
Davide
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