From: Gumbart, JC (
Date: Sat Mar 06 2021 - 17:02:07 CST

You might be able to hack the code of 3D-SNFG (made for representing glycans) to do what you want.;!!DZ3fjg!vB_lREJz5UjvHEJnAkx5eaWDvJGdF6oARgBVs6bzlPeHDI_Ew3V3IRxsWFpMTmX0Jg$;!!DZ3fjg!vB_lREJz5UjvHEJnAkx5eaWDvJGdF6oARgBVs6bzlPeHDI_Ew3V3IRxsWFpyNHJjyQ$


On Mar 6, 2021, at 2:58 PM, Johannes Haataja <<>> wrote:

Dear John,
ok - thank you for your reply. I guess there's no other MD
software (LAMMPS etc) that would offer a work around(?)

My best,

la, 2021-03-06 kello 12:46 -0600, John Stone kirjoitti:
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
arbitrary shapes for their particles, but they lost interest in
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.


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
only possible perhaps via importing STL files etc...?

My best,

PS: The reason I'm asking is that I would like visualize some hard
particle Monte Carlo simulations, cf.*3A*2F**2Fv3*2F__https*3A*2F**2Fen*2Flatest*2Ftutorial*2F00-Introducing-HOOMD-blue*2F07-Analyzing-Trajectories.html__*3B!!DZ3fjg!vONRATg-Q_EgeJPGdpUrZl8uZWbaXFQYQDtI4mJMReVOXnMGNZE-NH-DYSZ1HQ-bZg*24&amp;data=04*7C01*7Cgumbart**7Cf0febdceb57f44b888c908d8e0e418dc*7C482198bbae7b4b258b7a6d7f32faa083*7C0*7C0*7C637506617570481427*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=wAZ9AkPSue3f0cv*2Ff1iTWyytgOCkRbvsWleohWlAhmA*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!vB_lREJz5UjvHEJnAkx5eaWDvJGdF6oARgBVs6bzlPeHDI_Ew3V3IRxsWFoC3qBmfg$

and although VMD can read gsd trajectories, I haven't found a way
create custom particle shapes...