How to compare two similar structures?

In summary, the conversation discussed a simulation involving recrystallization and the identification of crystal A, amorphous crystal B, and crystal C. It was mentioned that crystal B is different from A and has been experimentally proven to be more similar to crystal C, although the recrystallization process is not apparent. The speaker has observed no significant differences in bond lengths, radial distribution functions, and coordination numbers between the amorphous, B, and C structures, possibly due to their low symmetry. The question posed was how to compare the amorphous, recrystallized crystal B with the known crystal C.
  • #1
only1892
6
0
I am doing some simulation like recrystallizaiton, crystal A-amorphous-crystal B. This crystal B is different from A and experimentally proved that B is more like crystal C. Even though the recrystallizaiton is not obvious. As far as I have done, the bond lengths and radial distribution functions,coordination numbers for amorphous,B and C have no huge differences. The reason for this is because the crystal B and crystal C both have low symmetry.

So my question is how to compare the amorphous, recrystallzed crystal B and the already known crystal C.
Thanks a lot..
 
Physics news on Phys.org
  • #2
I think you lost me somewhere in this story...

You have two atomic structures that are amorphous and you want to compare them?

Is that it or is there more?
 
  • #3


I would approach this question by first considering the properties and characteristics of both crystal B and crystal C. It is important to understand the differences and similarities between the two structures, such as their crystal lattice, atomic arrangement, and symmetry. This can be done through various analytical techniques, such as X-ray diffraction, electron microscopy, and spectroscopy.

Next, I would compare the results of the simulation of crystal B to the experimental data of crystal C. This would involve analyzing the bond lengths, coordination numbers, and other structural properties in both structures. If there are any significant differences, it would be important to understand the underlying reasons for them and how they may affect the overall behavior of the crystals.

In addition, it would be beneficial to consider the thermodynamic properties of both structures, such as their melting points and enthalpies. This can provide insight into the stability of each structure and how they may change under different conditions.

Furthermore, I would also explore the possibility of using computational methods, such as molecular dynamics simulations, to compare the two structures. This can provide a more detailed understanding of the atomic-level interactions and help identify any subtle differences between the two structures.

Overall, comparing two similar structures requires a comprehensive approach that combines experimental data, theoretical calculations, and computational simulations. It is important to consider all aspects of the structures and understand the underlying factors that contribute to their similarities and differences.
 

Related to How to compare two similar structures?

1. How do I identify the similarities between two structures?

To compare two similar structures, you can start by visually inspecting the structures for any obvious similarities. You can also use analytical techniques such as structural alignment or superposition to identify any shared features between the structures.

2. What is the best method for comparing two protein structures?

The best method for comparing two protein structures depends on the specific question you are trying to answer. Some commonly used methods include sequence alignment, structural alignment, and functional classification. It is important to consider the limitations and assumptions of each method and choose the most appropriate one for your research question.

3. Can I compare structures of different types of molecules?

Yes, it is possible to compare structures of different types of molecules. However, the methods and techniques used may vary depending on the type of molecules being compared. For example, comparing protein structures may require different methods than comparing DNA or RNA structures.

4. How can I determine the significance of the similarities between two structures?

The significance of the similarities between two structures can be determined by statistical analyses such as the Root Mean Square Deviation (RMSD) or the Z-score. These analyses take into account the size and complexity of the structures and provide a quantitative measure of the significance of the similarities.

5. Are there any software tools available for comparing two structures?

Yes, there are many software tools available for comparing two structures. Some popular tools include PyMOL, Chimera, and VMD, which offer various options for structural comparison and visualization. It is important to choose a tool that is suitable for your specific research question and data.

Similar threads

  • Atomic and Condensed Matter
Replies
1
Views
1K
  • Differential Geometry
Replies
0
Views
645
  • Atomic and Condensed Matter
Replies
1
Views
1K
  • Atomic and Condensed Matter
Replies
2
Views
2K
  • Biology and Chemistry Homework Help
Replies
1
Views
649
  • Atomic and Condensed Matter
Replies
1
Views
1K
  • Computing and Technology
2
Replies
41
Views
4K
  • Atomic and Condensed Matter
Replies
4
Views
2K
  • Atomic and Condensed Matter
Replies
11
Views
3K
  • Chemistry
Replies
1
Views
2K
Back
Top