id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
521	Problem positioning drawing copies	tic20@…	Tom Goddard	"Hi,

I've been messing around a lot with Places over the past couple of days, working at getting symmetry copies of a molecule to display as duplicates of the one Model object using the Model.positions property. I saw the following passage from the documentation at http://preview.cgl.ucsf.edu/chimerax/docs/devel/core/graphics/graphics.html#chimerax.core.graphics.drawing.Drawing:

""Multiple copies of a drawing be drawn with specified positions and colors. Copy positions can be specified by a shift and scale factor but no rotation, useful for copies of spheres. Each copy can be displayed or hidden, selected or unselected.""

Unless I'm misunderstanding something about the implementation, it would appear that the reason rotations haven't been working as expected is that somewhere in the Place pipeline the rotation matrix is getting transposed, so it's failing any time the matrix is non-symmetrical. Demonstration:

import numpy
from chimerax.core.geometry import Place
rot = numpy.array([[1, 0, 0],[1,-1,0],[0,0,-1]],numpy.double)
p = Place(axes = rot)
c1 = numpy.array([40, 50, 60],numpy.double)
c2 = numpy.array([c1])
c3 = numpy.array([c1])
c1 = numpy.matmul(rot,c1.transpose())
p.move(c2)
p.transpose().move(c3)

c1

   array([40., -10., -60.])


c2

   array([90., -50., -60.])


c3

   array([40., -10., -60.])


Cheers,

Tristan"	defect	closed	blocker		Graphics		invalid						all	ChimeraX