Hi Brian, This is not a direct answer to your question, but alternatives to showing VDW dots are: (A) show sphere representation (VDW spheres) instead of stick representation of atoms (B) show molecular surface, which will update as bonds are rotated. You could make it transparent and/or show it as mesh, e.g. commands: surftrans 75 surftrans 0 surfrep mesh There is also a “dot” style (as opposed to mesh and solid) but then you’d want to crank up the vertex density to put the dots closer together… e.g. select the surface with Ctrl-click and then use the Selection Inspector (open by clicking green magnifying glass icon), inspect: MSMS surface, increase “vertex density” and maybe dot size. Depending on the structure, however, molecular surface calculation may be slow and/or fail as you change the structure by rotating bonds. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 23, 2019, at 1:29 PM, Brian E Coggins <bec2@duke.edu> wrote:
Hello,
If I am displaying atomic dots using the “vdw” command, is there any way to get the dots to update as structural changes are made? For example, if I am adjusting torsions in the Adjust Torsion box, is there a way to get the dots to follow along as the structure changes?
Thanks, Brian
--- Brian E. Coggins, Ph.D. Assistant Research Professor of Biochemistry Duke University, Durham, NC