[Chimera-users] Update VDW Dots During Torsion Rotation

[Eric Pettersen]

Glad it did what you needed!

—Eric

> On Jan 24, 2019, at 11:29 AM, Brian E Coggins <bec2 at 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 at cgl.ucsf.edu <mailto:pett at 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 at cgl.ucsf.edu <mailto: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 <mailto: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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>> 
> 
> ---
> Brian E. Coggins, Ph.D.
> Assistant Research Professor of Biochemistry
> Duke University, Durham, NC
> 
> 
> 
> 

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