[Chimera-users] rotation of the molecule using plane and the axis ?

Eric Pettersen pett at cgl.ucsf.edu
Fri Oct 25 16:24:24 PDT 2013

On Oct 24, 2013, at 2:10 AM, Marek Maly <marek.maly at ujep.cz> wrote:

> Hello,
> if I define plane "p" using 3 atoms of the given molecule, is there
> any possibility to rotate consequently molecule into the position
> in which the chosen axis of the coordinate system (x or y or z) is perpendicular
> to the plane "p" ? (Of course except slow and not accurate "manual" rotation by mouse).

Hi Marek,
	My interpretation of your question is that you define a plane in one molecule, and then want to position another molecule so that it's X (or Y, or Z) axis is aligned with the normal of the plane (possibly also positioning the origin of the axis with the origin of the plane).  If I've misinterpreted the question, let me know.  Anyway, I've appended a Python script that does that.  You run it simply by opening it with File->Open or with the "open" command.
	It assumes you have exactly one plane defined, and that you want to move the model with the highest model ID so that its X axis is aligned with the plane normal and its coordinate system origin is coincident with the plane origin.  If you look at the script I think it's obvious how change X axis to other axes (though nothing else is obvious!).
	Hope this helps.


	Eric Pettersen
	UCSF Computer Graphics Lab

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