Hi Jingchuan, The markers from “measure center” are essentially fake atoms, and then if both things in the “measure distance” command are atoms (or makers) you are getting the distance from center to center. The distances are all in physical units, so if your data is in angstroms the distance will also be in angstroms. If the markers were based on some density map, you can check the physical scaling of that map by choosing “Features… Coordinates” in the Volume Viewer dialog and then looking at “Voxel size." You can doublecheck that it is the center-to-center distance by using the “distance” command that works on atoms but not surfaces: distance #13,14 … in other words, that should give the same number as your “measure distance” command. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Feb 9, 2016, at 5:31 AM, Jingchuan Sun <jingchuan@gmail.com> wrote:

Hello, I use "measure center #11 mark true radius 20" to make a ball to represent a model, then use "measure distance #13 #14 show true".

I get a number of distance between the two balls. Is it pixel value or angstrom? Is it between the center or surface of the two balls? Best, Jingchuan _______________________________________________ <a href="Chimera-users@cgl.ucsf.edu">Chimera-users mailing list</a> <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">Manage subscription</a>