Hi Andrew, Well, there are a couple of things going on: (1) perspective (closer things are bigger) (2) different radii for different atom types, when shown in “sphere” style (full VDW radius) or “ball” (scaled VDW radius) You can turn off perspective with command: set projection orthographic <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#projection> There are several ways to change VDW radii, including command “vdwdefine”… see the bottom section of this page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html> For example, to make all carbon atoms have radius 1.5, command: vdwdefine 1.5 C I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 10, 2019, at 7:46 AM, Andrew Garven <garvena@mcmaster.ca> wrote:
Hi,
I am trying to implement a script so that each individual atom in each molecule I view on chimera is the same size (ie each carbon atom i view, regardless of the size of the molecule views a the same size). I realize this must be a function of the scale factor which changes the size of the molecules to appropriate viewing size. Is there a way to properly scale each molecule so that they have a standard atom viewing size.
I would appreciate any help in this regard.
Andrew