On Jan 24, 2019, at 11:29 AM, Brian E Coggins <bec2@duke.edu> wrote:

Eric,

Hack or not, this does the job perfectly!  Many thanks.

Brian

On Jan 23, 2019, at 6:36 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Brian,

It seems the vdw command caches the computed surface points and that therefore various tricks with ~vdw/vdw don’t update the surface.  However changing the dot density does clear the cache and cause a recomputation, so you can use this awful hack to get the vdw surface to update as you adjust torsions:

perframe “vdwdens 5.1; vdwdens 5”

Every frame, the density will be changed to 5.1 and then back to the (default) 5.  You might want to use different numbers.  I prefer not to be “credited” with this idea. :-)

not Eric Pettersen

not from the UCSF Computer Graphics Lab

On Jan 23, 2019, at 3:14 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

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
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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

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Brian E. Coggins, Ph.D.

Assistant Research Professor of Biochemistry

Duke University, Durham, NC