VMD-L Mailing List

From: Shubham Agarwal (shubham.tifrh_at_gmail.com)
Date: Mon Dec 21 2020 - 09:58:35 CST

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.
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.
I can share one of my data files if it's unclear to you.

Looking forward to hearing from you soon.
Regards,
Shubham

On Thu, 17 Dec 2020 at 16:51, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> 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,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Dec 17, 2020 at 11:38:15AM +0100, Shubham Agarwal wrote:
> > Dear VMD Community,
> > I hope you are doing good and safe!
> > I have a query regardingĀ visualizing the two data sets. More
> > specifically, I want to visualize the wavefunction and the shape at
> the
> > same time. Is it possible to visualize these two data sets at the same
> > time using VMD!?
> > If yes, it would be very kind if you could explain a bit and /or
> share the
> > format of the file.Ā
> > Looking forward to hearing from you soon.Ā
> > Best,
> > 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>