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31 votes
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What are the freely available crystal-structure visualization softwares?

ASE The Atomic Simulation Environment (ASE) has visualization capabilities. It is a python environment that allows direct interaction with a lot of atomistic simulation tools. https://wiki.fysik.dtu....
Fabian's user avatar
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23 votes

What are the freely available crystal-structure visualization softwares?

pymatgen & ASE I'm a big fan of simplicity and integration in my python-based and Julia-based workflow. Therefore I typically directly use the visualisation features from pymatgen, such as ...
Michael F. Herbst's user avatar
22 votes

What are the freely available crystal-structure visualization softwares?

OVITO OVITO is a great tool for visualising supercells and simulation cells with a large number of atoms. There are plenty of modifications available that facilitate analysis, and it also has a Python ...
Mythreyi's user avatar
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20 votes
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How to calculate diffraction pattern from a model of unit cell?

Perhaps the easiest solution is to use VESTA, which can read in a CIF (and many other crystalline structure formats) and produce a powder diffraction pattern ("Utilities" > "Powder Diffraction Pattern"...
Andrew Rosen's user avatar
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20 votes

What are the freely available crystal-structure visualization softwares?

Jmol For visualisation there's also a standalone Java application Jmol, which has a GUI and a more powerful command-line "console". I particularly like it for quickly visualising vibrational ...
Phil Hasnip's user avatar
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20 votes

What are the freely available crystal-structure visualization softwares?

AtomEye My favorite for working with inorganic crystals. But I moved to biomolecules several years ago, so I don't know how it compares with newer programs. AtomEye has no menu. It is driven by ...
marcin's user avatar
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20 votes

What are the freely available crystal-structure visualization softwares?

OlexSys Olex2 For some applications there exists a elegant software called Olex2 which matches most of the crystallographic requirements of dealing with large systems like metal–organic frameworks.
SalvaCardona's user avatar
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18 votes

What are the freely available crystal-structure visualization softwares?

Avogadro Avogadro is generally considered to be a “molecular editor,” designed to construct and view molecules and materials in 3D. It's a cross-platform software. Even when its mainly used for ...
Anoop A Nair's user avatar
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17 votes
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How can I create a .CIF file from x-ray diffraction data in a paper, for compound not found in crystallographic database

You can use the free software VESTA for creating a new structure by following steps From the file menu choose New structure Go to Unit cell panel and choose the space group of the structure Enter ...
Thomas's user avatar
  • 9,132
16 votes

What are the freely available crystal-structure visualization softwares?

MERCURY Mercury is a specialized software to treat/manipulate crystal structures. It is part of the Cambridge Structural Database (CSD). From Mercury's site, it allows you to: Generate packing ...
Camps's user avatar
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16 votes
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How to build matter modeling models with appropriate tools?

Atomic Simulation Environment (Surfaces) I am going to narrowly cover surface models in this answer since ASE is more than capable of handling a wide range of models from nanoparticles, surfaces, 2D ...
Tristan Maxson's user avatar
15 votes

What are the freely available crystal-structure visualization softwares?

iRASPA fast & beautiful visualization of porous materials (but not only) Features according to https://iraspa.org/iraspa/ structure creation and editing, creating high-quality pictures and movies,...
leopold.talirz's user avatar
14 votes

What are the freely available crystal-structure visualization softwares?

XCrySDen Official website:http://www.xcrysden.org/XCrySDen.html XCrySDen is a crystalline and molecular structure visualization program aiming at the display of isosurfaces and contours, which can ...
Jack's user avatar
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13 votes

What are the freely available crystal-structure visualization softwares?

Beautiful Atoms Beautiful Atoms is a Python package for editing and rendering atoms and molecules objects using Blender. A Python interface that allows for automating workflows. Features: Model: ...
Xing's user avatar
  • 161
13 votes

What are the freely available crystal-structure visualization softwares?

VESTA You can try VESTA. It is good, lightweight and works on Windows and Linux platforms. It is good for viewing and production level image quality manipulation. https://jp-minerals.org/vesta/en/...
Pro's user avatar
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13 votes

What are the freely available crystal-structure visualization softwares?

Crystal Impact Diamond Crystal Impact Diamond, despite being a commercial product, offers a free demo-version. One can import a structure, adjust its appearance and use screen capturing software for ...
andselisk's user avatar
  • 245
12 votes

Extracting molecular structure from CIF file using VESTA or Mercury

VESTA I'm an avid user of VESTA and haven't quite used Mercury. So I'll the steps to do it in VESTA (it's quite easy though) Step 1: Open your file in VESTA Step 2: Choose the selection tool in the ...
Anoop A Nair's user avatar
  • 4,496
11 votes

What are the freely available crystal-structure visualization softwares?

MoleView Super lightweight Developed based on standard plotting library (Matplotlib) Very easy to install pip install moleview All-in-one command ...
High Performance Rangsiman's user avatar
11 votes

How may I create a CIF for a core-shell nanostructure? Is it possible in VESTA, or elsewhere?

Well, to answer properly this question first we would need a clarification about the nature of the CIF file. This type of file is Crystallographic Information File, which means that it is devoted to ...
SalvaCardona's user avatar
  • 1,590
10 votes

What are the freely available crystal-structure visualization softwares?

UnityMol Conceived with biological systems in mind, but relevant for any molecular system Modern interface: recent and still under active development Supported formats: ...
Hebo's user avatar
  • 1,675
10 votes
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acceptable range of stretching of a lattice unit cell when we do the heterostructure

I would like to add to Jack's answer that beyond the raw numbers of what an acceptable amount of strain may be, it can also be important to consider the physical situation of interest when matching ...
ProfM's user avatar
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10 votes

Problems with finding the unit cell from a CIF file and extracting XYZ coordinates using a software

If you haven't figured it out yet here is what I would've done using mercury to get the xyz file of the dimer. There is some disorder in the crystal structure which I think means that there are ...
Unskilled's user avatar
  • 361
9 votes
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Help understanding square root notation of supercell

The main idea here is to preserve the periodic boundary conditions when creating a fractional supercell. Therefore, not all combinations are possible, such as $\sqrt{2}\times\sqrt{2}$ or$\sqrt{5}\...
Shahid Sattar's user avatar
8 votes

How can I create a .CIF file from x-ray diffraction data in a paper, for compound not found in crystallographic database

The journal requires that the data is deposited in CCDC, ICSD or CRYSTMET. This one was apparently deposited in ICDC with the depository number CSD-417100 (the number is given in the paper, I don't ...
marcin's user avatar
  • 1,800
8 votes

acceptable range of stretching of a lattice unit cell when we do the heterostructure

There are lots of papers about the strain engineering of two-dimensional materials. For example: Strain-Engineering of Band Gaps in Piezoelectric Boron Nitride Nanoribbons Tuning Electronic and ...
Jack's user avatar
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8 votes
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Creating a heterostructure in VESTA

Since the constituent monolayers have generally differing lattice constants, special care is needed in the construction of the atomic models in such a way that the strain is minimized. Let us denote ...
Jack's user avatar
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8 votes

How may I create a CIF for a core-shell nanostructure? Is it possible in VESTA, or elsewhere?

Two things are mixed in the question. How to create atomistic model of a core-shell nanoparticle? Are both the core and the shell assumed to be crystalline? Most likely you will need is to write a ...
marcin's user avatar
  • 1,800
8 votes

What are the freely available crystal-structure visualization softwares?

nglview and nvc Recently I found it hard to make the pymatgen structure_vtk visualization method to work. I believe it might be deprecated in favour of ...
Maurits Houck's user avatar
7 votes
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How are the simulated powder diffraction patterns calculated in CCDC Mercury?

Program's website has this question in FAQ, but it doesn't provide an answer, only refers to a standard textbook. The program doesn't use Debye's formula. This formula uses whole crystal (thousands or ...
marcin's user avatar
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