I am struggling to see why one would want to apply an improper rotation, which I thought was defined as rotation plus reflection. Det=-1. Truly bad things happen to ones amino acids.
Unless you had the coordinates from a small mol in one chiral arrangement, and wanted it in the other? But in that case just changing the sign of all the atomic coordinates would achieve the same. Adrian Sent from my iPhone > On 12 Mar 2018, at 12:43, Tristan Croll <ti...@cam.ac.uk> wrote: > > Assuming you have a good reason for this, you can apply any arbitrary > transform fairly straightforwardly in ChimeraX. In the console > (Tools/General/Shell), and assuming your model is the only one loaded: > > m = session.models.list()[0] > import numpy > transform_matrix = numpy.array([[r11, r12, r13, tx], [r21, r22, r23, ty], > [r31, r32, r33, tz]]) > from chimerax.core.geometry import Place > transform = Place(matrix=transform_matrix) > m.atoms.coords = transform.moved(m.atoms.coords) > > ... which could of course be extended into a script to loop over many > models/transforms with a bit more work. > > Hope this helps, > > Tristan > >> On 2018-03-12 10:24, Phil Evans wrote: >> The command ROTATE in pdbset should allow to apply any valid rotation >> matrix, ie determinant = +1.0 >> Anything else will distort the coordinates >>> On 12 Mar 2018, at 10:13, Franck Coste <franck.co...@cnrs-orleans.fr> wrote: >>> Hi all, >>> I'd like to apply an improper rotation matrix to PDB files but it seems >>> it's not allowed in pdbset. Does anyone know a program where I could do >>> this ? >>> Thanks in advance. >>> Regards, >>> Franck. >>> -- >>> <Signature.JPG>
