VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
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
(https://www.ks.uiuc.edu/Research/vmd/plugins/mdff/), 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.

-Josh

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
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io