Re: [IMP-users] Geometrical Transformations and their effects in written files

[Ben Webb <>]

On 5/31/17 2:23 PM, Kai Karius wrote:
> cx = IMP.core.XYZ(c.get_hierarchy())
> IMP.core.transform(cx,g)
> IMP.atom.write_pdb(s.get_hierarchy(),"test_1.pdb")
>
> g rotates the clone around some axis specified elsewhere. When I look at 
> the file I would expect two molecule in different positions, yet they 
> sit on top of each other. What am I missing?

There are two transform functions:

IMP.core.transform() applies a transformation to an XYZ particle.

IMP.atom.transform() applies a transformation to a Hierarchy.

I'm pretty sure you want the second one, since it will move all atoms 
(or other geometric objects) in the hierarchy (which is what you want) 
rather than just the declared "center" of the top-level hierarchy particle.

	Ben
--
                      https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle