VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 07 2021 - 14:55:31 CST

Hi,
  I think JC's suggestion is by far the most pragmatic way to
move forward with what you need to get done. If you encounter
trouble developing your own script, let us know.

Best,
  John Stone

On Sun, Mar 07, 2021 at 02:31:07PM +0000, Johannes Haataja wrote:
> 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...
> > > > >
> > > >
> > > >
> > >
> >
> >
> 

-- 
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/