On Oct 24, 2013, at 2:10 AM, Marek Maly <marek.maly@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 Eric Pettersen UCSF Computer Graphics Lab