From: Josh Vermaas (
Date: Wed Oct 05 2022 - 16:51:57 CDT

Hi Max,

To make the surfaces into STL files, you can use the rendering
interface. However, you want a volume, so I think what you want is to
abuse the ability for VMD to make density maps from molecular
geometries. The MDFF plugin is what I'm most familiar with
(, using mdff sim
with appropriate arguments to recapitulate what I see on the screen
using a quicksurf representation. Note that you will need to choose a
threshold value, since the dx files that you generate will have non-zero
entries pretty far away from actual atomic densities.


On 10/5/22 4:13 PM, Max Win wrote:
> Hi All,
> I am wondering how I can take the output of a QuickSurf representation
> function and convert it into a voxel-based file (NetCDF) or a STL file
> (NetCDF) for further analysis. Would this be possible in a tcl script
> with defined atomic radii? Attached is an example snapshot of
> QuickSurf representation I would like to turn into a STL or Voxel file.
> image.png
> Best,
> Max

Josh Vermaas
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University