[Chimera-users] Update VDW Dots During Torsion Rotation

Eric Pettersen pett at cgl.ucsf.edu
Wed Jan 23 15:36:54 PST 2019

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 at 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
> -----
> 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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