From: John Stone (
Date: Wed Dec 01 2021 - 00:55:03 CST

  You could easily calculate the bounding box for your system using
built-in VMD measure commands and then draw whatever absolute scale
you like using the VMD "draw" or "graphics" commands. If you use
an orthographic projection, then so long as you position the
scale-bar or similar geometry closer to the camera than the molecule,
it will be visible and will match the molecular structure's scale.
Make sure to draw into the same molecule and not create a note one
just for the scale bar graphics, because creating a new molecule
just for the graphics objects can lead to a different scale transformation
matrix. Of course, one can set all of the molecules with a consistent
set of view transformation matrices if you start doing things that require
more sophistication, but I'm just trying to suggest the easiest possible
route to the result you're after.

There should be no need to draw the frame or label geometry after the fact,
you can do it in VMD itself quite easily.

  John Stone

On Thu, Nov 25, 2021 at 02:50:20PM +0100, Philip Loche wrote:
> Dear all!
> I am currently facing the problem of rendering a lot of systems in an orthographic representation.
> Examples are snapshots in time of a lipid bilayer simulation.
> To get a more quantitative view of processes happening at the lipid bilayer, I would like to add a
> ruler/frame to the system. I know that there exist the ???Ruler??? extensions in VMD. However, this
> ruler only shows me relative length scales and not the absolute limits of my current view. One
> workaround would also be extracting the limits of the atomic positions in my current view and
> plotting the frame with an external library after the render process.
> Thanks for your help!
> Philip
> ???
> Philip Loche
> Department of Physics
> Freie Universitšt Berlin
> Arnimallee 14, Room 0.3.30
> 14195 Berlin, Germany
> phone: +49 (0)30/838-55279

NIH Center for Macromolecular Modeling and Bioinformatics
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