From: Lee-Ping Wang (
Date: Fri Feb 28 2014 - 23:03:01 CST

Hi Ben,

Sorry for the extra email. On occasion I want to add extra bits into my VMD visualization to highlight stuff, hence the polyhedra and circles questions. I have thought about using triangles to draw polyhedra, but the higher level wrapper for drawing, say, a dodecahedron could become quite complex (especially if I want to use surface normals to make them look nice).

I realize it's beginning to go outside the scope of what VMD was designed to do, but my experience so far is that VMD can be amazingly flexible when we take advantage of the scripting interface and available command line tools.


- Lee-Ping

On Feb 28, 2014, at 7:57 PM, Benjamin Kaduk <kaduk_at_MIT.EDU> wrote:

> Hi Lee-Ping,
> On Fri, 28 Feb 2014, Lee-Ping Wang wrote:
>> 1) Drawing circles. I have the following TCL snippet for drawing a
>> circle but it's kind of slow. I could also use VMD spheres with
>> angle-modulated transparency, but in this case I would prefer for it to
>> simply be a circle.
> [snip]
>> 2) Drawing small polyhedra. My method is to create atoms at the
>> positions of the vertices and use the "Polyhedra" representation. However,
>> VMD complains that there are too many bonds and does not draw all of the
>> polyhedral faces.
> I think you get to use the 'triangle' primitive for drawing generic polyhedra. (Wrapped in some higher-level functions, of course.)
> With respect to circles, I don't have any good ideas. It's good to keep in mind that VMD is primarily a molecular visualization tool, and is not really intended to (also) be a generic drawing tool.
>> 3) Tooltips. Is it possible to pop up an image if I mouse-over an atom
>> or graphics object?
> I don't know, sorry.
> -Ben