VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 31 2020 - 11:53:09 CST

Hi,
  Have you worked through any of the VMD tutorials yet?:
    http://www.ks.uiuc.edu/Research/vmd/current/docs.html#tutorials

I think that you should be able to visualize all of the properties
you're interested in, using the Isosurface representation, along with
some of the standard space filling atomic structure representations.

If you have worked through the tutorials, particularly the quantum
chemistry related ones, and you still have questions, let me know.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 21, 2020 at 04:58:35PM +0100, Shubham Agarwal wrote:
> Dear Dr John E. Stone,
> Thanks for your response. I hope you are doing well, and safe!
> I am trying to open the wavefunction/isosurface with the shape. This shape
> data is from the .dx file.Â
> Actually, we are using our own codes/methods to calculate the
> wavefunction. This method is called, SLCBB (Strain Linear combination of
> bulk bands), which generates the wavefunction in .lat file and shape in
> .dx file. So, I have created a .xsf file in which the atomic position,
> wavefunction and the shape data (from .dx file, which I converted into a
> single column data) is given. And I am trying to open both of the data
> sets at the same time in VMD.Â
> I can share one of my data files if it's unclear to you.Â
> Looking forward to hearing from you soon.Â
> Regards,
> Shubham
> On Thu, 17 Dec 2020 at 16:51, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â It's unclear from your email exactly what you mean by visualizing
> the "wavefunction and the shape" at the same time. I suppose you're
> asking about displaying molecular orbitals and ball-stick models?
> If so, then the answer is yes. I would suggest working through the
> available VMD tutorials to become more familiar with how it works.
> You haven't specified what quantum chemistry software you're using
> so I can't give you any specific guidance, since the approach differs
> depending on whether you're using a plane wave code or a code
> based on Gaussian type orbitals. If we knew more about what software
> you're using we could probably give further suggestions about the best
> way to load associated files, etc.
>
> Best regards,
> Â John Stone
> Â [2]vmd_at_ks.uiuc.edu
>
> On Thu, Dec 17, 2020 at 11:38:15AM +0100, Shubham Agarwal wrote:
> >Â Â Dear VMD Community,
> >Â Â I hope you are doing good and safe!
> >Â Â I have a query regardingÄ* visualizing the two data sets. More
> >Â Â specifically, I want to visualize the wavefunction and the shape
> at the
> >Â Â same time. Is it possible to visualize these two data sets at the
> same
> >Â Â time using VMD!?
> >Â Â If yes, it would be very kind if you could explain a bit and /or
> share the
> >Â Â format of the file.Ä*
> >Â Â Looking forward to hearing from you soon.Ä*
> >Â Â Best,
> >Â Â Shubham
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [3]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [4]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/~johns/
> 4. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/