Nearest neighbour, nnn....etc. of an atom in a crystal

In summary, the conversation is about the use of software for visualizing crystal or protein structure, specifically VESTA and PyMol. The user is interested in finding out how many atoms are the nearest and next nearest neighbors of a selected atom and if there is any software or data book that can provide this information. The expert mentions that PyMol is the standard software for protein crystal structures and that distances can be measured using the "distance" command and neighboring atoms can be found using the "around" command. The conversation ends with the user expressing difficulty in exiting the program and the expert explaining that it is a command-based program that may have evolved from an older version.
  • #1
qnach
143
4
There are some software can provide visualization of crystal or protein structure, i.e. VESTA.
I want to know how many atoms is the nearest neightbour (and their distance), and the next nearest neighbour...etc of a particular atom.
Is there any software (or perhaps some data book?) can do this?
 
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  • #3
Ygggdrasil said:
The standard software for looking at protein crystal structures is PyMol: https://www.pymol.org/

You can measure distances with the "distance" command, and find atoms neighboring a selected atom using the "around" command:
https://pymolwiki.org/index.php/Distance
https://pymolwiki.org/index.php/Selection_Algebra
Thanks, I have got this program. Could it also be used for crystal structures?
But don't know how to exits from it, except restart my computer...
It is not a window version. Perhaps evolved from some program 20 years ago and still in command mode...
 

FAQ: Nearest neighbour, nnn....etc. of an atom in a crystal

1. What is the nearest neighbour of an atom in a crystal?

The nearest neighbour of an atom in a crystal is the atom that is located closest to it in terms of distance. This can vary depending on the crystal structure and arrangement of atoms.

2. How is the nearest neighbour of an atom in a crystal determined?

The nearest neighbour of an atom in a crystal is usually determined through mathematical calculations based on the lattice parameters and atomic positions in the crystal. This can also be determined experimentally through techniques such as X-ray diffraction.

3. What is the significance of knowing the nearest neighbour of an atom in a crystal?

Knowing the nearest neighbour of an atom in a crystal is important for understanding the structural and chemical properties of the crystal. It can also provide insights into the bonding and interactions between atoms in the crystal.

4. Can the nearest neighbour of an atom in a crystal change?

Yes, the nearest neighbour of an atom in a crystal can change if the crystal structure undergoes a phase transition or if the crystal is under external stress or temperature changes. However, the number of nearest neighbours for each atom in a crystal is usually constant.

5. How does the concept of nearest neighbour relate to crystal lattice structures?

The concept of nearest neighbour is directly related to crystal lattice structures as it describes the arrangement of atoms around a central atom in the lattice. The types and number of nearest neighbours can vary depending on the type of lattice structure, such as simple cubic, face-centered cubic, or body-centered cubic.

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