[PyMOL] Align with axis and rewrite coordinates

[Reed, C. (creed) <cr...@br...>]

Is there a way to open a crystal structure and realign the structure with an axis, then save the transformed coordinates?  I want all atoms to remain in the same position with respect to each other...just not with respect to the crystallographically defined x, y, z.  I have tried alter_state command with rebuild....but I only seem to be able to find commands that translate along the x, y, z. The rebuild does rewrite the coordinates, so that bit is working.  I have tried rotating, but this only rotates around an already defined axis.  I need to move the structure away from the predefined axis positions; the easiest way I could think would be to align with a current axis, but open to other ideas. For example, if there is a way to incorporate sine and cosine into the alter_state function...

Thanks in advance!


Carly R. Reed
Associate Professor and Advisement Coordinator
SUNY Brockport
Department of Chemistry and Biochemistry
(585)395-5588 (office)
(330)575-6754 (cell)