Questions tagged [visualization-software]

Questions regarding the various types of visualization software for materials modeling.

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Creating a Hypothetical Hexagonal Monolayer Structure Similar to MoS2

I am seeking guidance on how to generate a POSCAR file for a hypothetical monolayer with a hexagonal structure similar to MoS2. Can anyone provide me with a step-by-step procedure or recommend any ...
Farah Shehzadi's user avatar
5 votes
2 answers
875 views

How may I reproduce chemical structure drawings?

I would like to draw the following structures: How many I do it?
SOELHADFI's user avatar
  • 431
1 vote
0 answers
8 views

checkcif and PLATON ellipsoid plot: crystall structure does not look right

When I open my CIF file in VESTA it looks ok. When I upload it to https://checkcif.iucr.org/, the ellipsoid plot produced by PLATON does not look right. The unit cell of the supercell is not fully ...
freude's user avatar
  • 382
4 votes
1 answer
59 views

Povray rendering of Jmol visualization appears brighter

I would like to use Povray to render nice-looking graphics of molecules, which can be exported from visualization softwares like Jmol. However, I have noticed that the color of the rendered graphics ...
Jingyang Wang's user avatar
2 votes
1 answer
50 views

Visualizing magnetic moments of Quantum espresso input/output files

I am looking for a software/website that can visualize atomic structure of my quantum espresso input/output files with magnetic moments. Any help will be highly appreciated. Thanks in advance!
rahman62's user avatar
  • 143
3 votes
1 answer
127 views

XCrySDen installation

After installing xcrysden, I have this output when trying to launch the software: ...
mle's user avatar
  • 989
5 votes
2 answers
72 views

ASE: How to plot the irreducible Brillouin zone and this bandpath from a bandpath object

I am using ASE (Atomic Simulation Environment) for theoretical chemistry and I see an option to plot the irreducible Brillouin zone and this bandpath but I can't figure out how. I'm not a programmer. ...
Samaray's user avatar
  • 61
1 vote
0 answers
17 views

Removing "say XYZ.PRF:" name in winplotr in Fullprof?

I am facing difficulty on removing text like XYZ.PRF:, when we run fullprof in External applications in WinPLOTR. Is there some way to remove it?
Anshul Sharma's user avatar
5 votes
0 answers
87 views

Color of isosurface in charge density visualization

I am trying to visualize the charge density of a crystal through VESTA. However the intersection surface of the isosurface and the boundary turns into blue, which is certainly not included in my ...
蕭力諶's user avatar
  • 411
3 votes
0 answers
107 views

Advise in generating ESP surfaces from Gaussian .cube files using the IQmol software

I am trying to generate an ESP surface of a Gaussian09 calculation using the iqmol software. I have used Gaussview to visualize the ESP surface by generating .cube files from .fchk files (using the ...
Kevin Freddo's user avatar
4 votes
0 answers
52 views

How to load xcrysden GUI in OSX after installing through Macports?

I am using MacOS Ventura, and would like to use xcrysden to visualize my Quantum espresso input and output files. For that, I have installed xcrysden on using Macports. But I am not able to laod the ...
rahman62's user avatar
  • 143
3 votes
1 answer
204 views

Rendering Vector Graphics Images

I am trying to render few representative structures for molecules. The requirement for the images is as follows: (1) It must be vector graphics, and (2) Atom colorings must intuitively make sense (...
Hemanth Haridas's user avatar
5 votes
2 answers
355 views

How to visualize a slice of the unit cell?

I have a cell that contains a sphere of organic molecules in a cube of water. What tool and how could I visualize the central cut (slice) of the unit cell? Similar to the one visualized in packmol ...
Dmitry Eremin's user avatar
6 votes
1 answer
93 views

How to address 'saveGraphic: Method not found' error in automating the generation of figures in avogadro using Python?

My question is a follow-up question to this question posted by Hemanth Haridas. I ran the example .py script in Geoff Hutchison's answer for the above mentioned question to generate .png files from ....
Aimun Jawed's user avatar
7 votes
1 answer
114 views

Is there a way to automate generation of figures from Avogadro?

I have a collection of molecules represented by SMILES codes, along with their corresponding 3D coordinates. I want to efficiently generate figures for these structures using Avogadro. Ideally, I ...
Hemanth Haridas's user avatar
3 votes
1 answer
513 views

How to find the smallest distance between 2 residues in Pymol?

I am very new to Pymol and was trying to figure out how I can find the largest distance between 2 residues. Using just the basic distance function I get multiple distances which is not very useful in ...
Faheem Azeemi's user avatar
4 votes
2 answers
180 views

Visualising the spatial distribution of water structure using VMD

I am trying to recreate Fig. 5b of this paper I have a solvated NH4+ in my system and would like to create a similar visualisation for my case. Can this be generated using VMD? If so could someone ...
Priyanshu Gupta's user avatar
5 votes
1 answer
456 views

Visualise bonds in ASE

I want to visualize an MD trajectory produced with ASE. ase.visualize.view produces an output for atoms and trajectories. I am not able to show the bonds between atoms. For atoms, I can use this in ...
Marco Di Gennaro's user avatar
1 vote
1 answer
196 views

How to build (visualize) 3x3x1 rectangular from 1x1x1 hexagonal unit cell of graphene by using VESTA

How can I build a 3x3x1 rectangular supercell from the hexagonal unit cell of graphene by using VESTA?
ahmed hassan's user avatar
8 votes
3 answers
747 views

Duplicate structure in PDB format?

I have a PDB file. I want to duplicate this pdb file automatically instead of doing it manually. For example, if I visualize my PDB, I will find only one structure in (x,y,z). I want to have more ...
Abd-Elazeem Mohamed's user avatar
8 votes
1 answer
1k views

Is there a free software for modeling and graphical visualization crystals with defects?

At real situation, it can happen, that a crystal can have defects, for instance, some of them are point defects — Schottky, Frenkel defects, line defects — dislocations, planar defects — grain ...
SFriendly's user avatar
  • 877
3 votes
1 answer
85 views

Adjusting y-axis of CASTEP band structure plots

when I produce a band structure plot using XMGRACE after running a CASTEP Bandstructure calculation I would like to have the bottom of the band gap to be zeroed. Is there an easy way to shift the axis,...
Rory Ward's user avatar
  • 121
3 votes
1 answer
63 views

Do I have to use Rwp, RI, Rf and atomic displacement parameter B to create a CIF file?

I want to create the CIF file of CuI using VESTA software.I used the following parameters to create my CIF : space group, lattice parameter, the angles (alpha, beta and gamma), atomic positions of Cu ...
Camilla's user avatar
  • 2,049
1 vote
0 answers
25 views

Can CrystalFp library be used to compare structures with different number of atoms? [duplicate]

Can I use CrystalFp library to analyze different structures (e.g. of Ca2Si04) that don't have the same number of atoms? I want to compare e.g. structure_1 with composition [2,1,4] and structure_2 with ...
leire's user avatar
  • 183
4 votes
0 answers
107 views

Which is the best way to display bonds?

We know that bonds, per se, are only characterized after topological studies but their visualizations is an easy and fast way to see if there are "connections" between some particles. I ...
Camps's user avatar
  • 22.9k
4 votes
1 answer
299 views

Is there any free software that helps to know specific charge densities or ELFs at any position of the material?

Can anyone suggest some free software that can visualize the charge density and/or electron localization function (ELF)? More importantly, can we determine/know those values (charge density and/or ELF)...
Sak's user avatar
  • 889
2 votes
0 answers
154 views

"Gview.exe" in Linux is not responding [closed]

I successfuly installed g16 and gview6 under fedora linux , the issue that I have is when I open gview after few seconds it stopped and a message is displayed on my screen
diamond999's user avatar
5 votes
1 answer
256 views

How to apply colors and graphics to VMD from Tcl?

I have a collection of pdb files (15), and I want to basically apply the same visualization settings on each one of them and render the image. I want the above settings, with a certain, resolution ...
megamence's user avatar
  • 4,141
6 votes
2 answers
951 views

A python compatible GUI chemical drawing library/software

So, I am developing a GUI for a python computational chemistry software (with PyQt5). The Qt part of the GUI will handle running the python software (calling the proper functions with proper arguments ...
S R Maiti's user avatar
  • 6,741
3 votes
0 answers
39 views

How to visualize the basis in the unit cell of crystals?

Usually, the unit-cell of a crystal is made up of lattice points and basis, but all the crystallography software like VESTA doesn't show the basis, is there any ...
Jack's user avatar
  • 1,997
2 votes
1 answer
86 views

Why is my pdb looking so weird? [closed]

I have generated the following pdb file for a polymer: ...
megamence's user avatar
  • 4,141
1 vote
1 answer
93 views

Suggestion for getting a type of plot

I am planning to use python to get a plot like this . But, I am only able to get this, So, I would appreciate it if someone helps me with this issue, (Maybe how to format the data): How to have ...
Saha_1994's user avatar
  • 969
6 votes
1 answer
104 views

A question about plotting: how to plot octahedrons as well as d orbitals effectively?

How to effectively plot an octahedron along with the $d$ orbitals of the metal atom at the center of the octahedron? Here is an example What kind of software can be used to draw this illustration? I'...
meTchaikovsky's user avatar
5 votes
1 answer
86 views

How to modify Gaussian Z-matrix to adjust distances between monomers

I am trying to make a script to adapt and modify the distances between two monomers I do have. I have build a xyz structure and use Openbabel to construct the Z-matrix of the system. However, I am not ...
Paul Logan's user avatar
5 votes
0 answers
72 views

Ask tips: For merging small figures into a big one with high resolution [closed]

my question is not related to material or modeling, but I guess many people in this community face it. I took a figure of a crystal structure by cropping the VESTA app on my laptop screen; band and ...
Binh Thien's user avatar
  • 2,035
5 votes
1 answer
506 views

How to create the vector image of crystal structure?

I am trying to create a vector image of TiO2 crystal because all journals require vector images. When I build the model for calculation, I use ...
Jack's user avatar
  • 1,997
4 votes
1 answer
232 views

How to save the generated 3d representation of the structure(s) by Viewer3d in Py4vasp?

I used py4vasp to calculate structure from data and then I displayed them in a structure viewer (Viewer3d) by this line: calc.structure[:].plot(). It returns a ...
Aaryan Tavakoli's user avatar
3 votes
0 answers
478 views

Atomic Simulation Environment (ASE) is unable to read a big trajectory file [closed]

The problem that I face is the ASE software can't read the trajectory file and throws this error ValueError: buffer is smaller than requested size. My assumption is ...
Saha_1994's user avatar
  • 969
8 votes
2 answers
272 views

Limits of periodic box from pdb

I have a pdb file of some solvent molecules in a box of 20 Angstroms I have built using Tinker. I have opened the file with Chimera, Molden, Pymol and Avogadro... but I would like to see, and maybe ...
Paul Logan's user avatar
6 votes
4 answers
3k views

Unable to install P4Vasp

I am currently learning how to use VASP and was looking at how to get the DOS plots. I have been recommended to use P4VASP but due to some reason I am not able to install it on my Ubuntu 20.04. When I ...
Parmeet Singh EP 066's user avatar
10 votes
1 answer
1k views

Best software to plot Charge densities

I have obtained cube files of charge density difference using Quantum Espresso. I am trying to plot these as a contour plot in an aesthetically pleasing manner with good quality. I'm aware that ...
ansonthms's user avatar
  • 921
5 votes
0 answers
741 views

xcrysden on a macOS Monterey [closed]

It seems that Xcrysden is the best software to visualize quantum espresso files. I've followed the directions from Xcrysden and was able to install it on macOS Monterey using MacPorts. However, I ...
ziulfer's user avatar
  • 231
10 votes
0 answers
1k views

How to visualize natural atomic orbitals from PySCF [closed]

I'm trying to visualize the different methods of getting localized orbital (LO) given in the User Guide. I went through the example, saved the orbitals as cube files, then opened the files in ...
Steve Cox's user avatar
  • 303
6 votes
1 answer
2k views

How to add a bond between two atoms in VMD?

I want to add a bond between specific atoms. I found on VMD page that one can use topotools (e.g. topo addbond 1 2 ), but I have a lot of residues so this method ...
Abd-Elazeem Mohamed's user avatar
7 votes
1 answer
223 views

How to move atom coordinates along a normal mode given the eigenvector?

I need to displace atoms along a complicated normal mode involving many atoms. I have the normal mode eigenvector, I just don't know how to turn the eigenvector into an algorithm to translate the ...
user avatar
4 votes
0 answers
151 views

Why extra lines in PDOS plot using xmgrace [closed]

Input file for 221 MoS2 &projwfc prefix = 'MoS2', outdir = './out', deltae = 0.1, filproj = 'MoS2-pdos.dat', Another file run ...
user4777's user avatar
10 votes
1 answer
1k views

Tools to Visualize Phonons

Software such as ChemCraft or GaussView is easy to find for vibrational calculations in gas phase, but I am finding it much more difficult to find good visualization software for phonons. I have ...
Tristan Maxson's user avatar
6 votes
1 answer
1k views

How to visualize protein-ligand complex MD run using VMD

GROMACS version: gmx, version 2021.4 GROMACS modification: No I'm following the Protein-Ligand Complex tutorial. I'd like to visualize the binding using VMD. I use the output from these commands: <...
littleworth's user avatar
  • 1,674
9 votes
5 answers
726 views

Recommended software to open NetCDF files?

I found plenty of packages that open .nc files but all specifically catered to climate (meteorological) and geo-maps data. I would like to get suggestions of ...
Camps's user avatar
  • 22.9k
14 votes
3 answers
2k views

How can I use a GUI on a supercomputer?

I am trying to make plots based to VASP simulation results, but I am struggling with how to download so much data from the server. A lot of examples on the internet are taught using the local desktop ...
Jack's user avatar
  • 1,997