VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Mar 06 2021 - 12:46:29 CST

VMD has a so-called "lattice cube" representation which was added
for the benefit of Lattice Microbes visualizations, but that is the
only other shape it currently allows for particles by default.

I had hoped to work with the HOOMD team to add support for visualizing
arbitrary shapes for their particles, but they lost interest in collaborating
after they began writing their own visualization code.
Since I don't know anything about their file formats or requirements
for such a feature, it's not something I would undertake on my own
without their involvement.

Best,
  John

On Sat, Mar 06, 2021 at 12:27:04PM +0000, Johannes Haataja wrote:
> Dear all,
> is it possible in VMD to visualize individual atoms using
> custom shapes e.g cubes or tetrahedrons, instead of VDW spheres? Or is
> only possible perhaps via importing STL files etc...?
>
> My best,
> Johannes
>
> PS: The reason I'm asking is that I would like visualize some hard
> particle Monte Carlo simulations, cf.
>
> https://urldefense.com/v3/__https://hoomd-blue.readthedocs.io/en/latest/tutorial/00-Introducing-HOOMD-blue/07-Analyzing-Trajectories.html__;!!DZ3fjg!vONRATg-Q_EgeJPGdpUrZl8uZWbaXFQYQDtI4mJMReVOXnMGNZE-NH-DYSZ1HQ-bZg$
>
> and although VMD can read gsd trajectories, I haven't found a way to
> create custom particle shapes...
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/