VMD-L Mailing List

From: Johannes Haataja (jh2225_at_cam.ac.uk)
Date: Sun Mar 07 2021 - 08:31:07 CST

Aah,
        much obliged - the scripting implementation doesn't seem too
hard to adapt for my purposes.

My best,

- J.

la, 2021-03-06 kello 23:02 +0000, Gumbart, JC kirjoitti:
> You might be able to hack the code of 3D-SNFG (made for representing
> glycans) to do what you want.
>
> https://urldefense.com/v3/__http://glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-for-glycans-3d-snfg/__;!!DZ3fjg!o72Jn1QPR9Itz-KYQg62qFTSoVPYBHNfaDr3IyYSRXl0Mbmn7syZGnWrWjfvvfDEgA$
> https://urldefense.com/v3/__https://pubmed.ncbi.nlm.nih.gov/27514939/__;!!DZ3fjg!o72Jn1QPR9Itz-KYQg62qFTSoVPYBHNfaDr3IyYSRXl0Mbmn7syZGnWrWjeLPZmDGA$
>
> Best,
> JC
>
> > On Mar 6, 2021, at 2:58 PM, Johannes Haataja <jh2225_at_cam.ac.uk>
> > 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,
> > Johannes
> >
> > 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
> > > 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://nam12.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fhoomd-blue.readthedocs.io*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*40physics.gatech.edu*7Cf0febdceb57f44b888c908d8e0e418dc*7C482198bbae7b4b258b7a6d7f32faa083*7C0*7C0*7C637506617570481427*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C1000&amp;sdata=wAZ9AkPSue3f0cv*2Ff1iTWyytgOCkRbvsWleohWlAhmA*3D&amp;reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!DZ3fjg!o72Jn1QPR9Itz-KYQg62qFTSoVPYBHNfaDr3IyYSRXl0Mbmn7syZGnWrWjdn125fcg$
> > > >
> > > > and although VMD can read gsd trajectories, I haven't found a
> > > > way
> > > > to
> > > > create custom particle shapes...
> > > >
> > >
> > >
> >
>
>