VMD-L Mailing List

From: Rafael Bernardi (rcbernardi_at_auburn.edu)
Date: Mon Dec 21 2020 - 12:16:45 CST

Dear Shubham,

I think in your case it would be easier if would share an image of what you want to make with VMD. Something that you found in a paper or that you prepared with another software.

I was curious and I tried to find what you are describing. I could not find anything that looked like a molecule.

Best

Rafael

……………………………………………………………………...
Rafael C. Bernardi
Biophysics Cluster - Department of Physics at Auburn University
NIH Center for Macromolecular Modeling & Bioinformatics
rcbernardi_at_auburn.edu<mailto:rcbernardi_at_auburn.edu>
rcbernardi_at_ks.uiuc.edu<mailto:rcbernardi_at_ks.uiuc.edu>
www.ks.uiuc.edu/~rcbernardi<http://www.ks.uiuc.edu/~rcbernardi>
+1 (334) 844-4393





From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Shubham Agarwal <shubham.tifrh_at_gmail.com>
Date: Monday, December 21, 2020 at 11:02 AM
To: John Stone <johns_at_ks.uiuc.edu>, Shubham Agarwal <shubham.tifrh_at_gmail.com>, "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Qurry Regarding Vizualization of two data sets

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<mailto: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<mailto: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/