[Chimera-users] Update VDW Dots During Torsion Rotation

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 23 15:14:33 PST 2019

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 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 at 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

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