Hi Sam, XYZ coordinates such as from "getcrd" are in the physical distance units of your dataset, most likely angstroms (not pixels or grid indices). Also (looking in that cryosparc guide) if you were also using "measure center," note that the ChimeraX implementation of "measure center" reports the center location in both grid indices and xyz coordinates. Example Log contents from ChimeraX: measure center #2 Center of mass grid index for 2gbp map 4 = (10.83, 9.99, 11.02) Center of mass xyz scene coordinates for 2gbp map 4 = (37.37, 30.58, 49.61) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 24, 2023, at 3:33 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am trying to determine the coordinates of a point on a volume for use in cryoSPARC (as described here for Chimera: Job: Local Refinement (Legacy) - CryoSPARC Guide). I was wondering if the getcrd command returns coordinates in angstroms (as it did in Chimera) or whether they are in pixels? This was not specified on the getcrd documentation page as far as I could see (Command: getcrd (ucsf.edu)). KR, Sam