I have a structural information (in Cartesian coordinate system) of a small molecule. According to the literature, one unit cell contains three molecules. I have set the parameters of the unit cell such as space symmetry, a and c. How can I set the atomic positions of my molecule in the next step? As I know, those positions should be written in fractional coordinate system other than Cartersian coordinate system. What's more, how can I set the orientation of 3 molecules in one unit cell? Is there any rule to follow?
Please try to locate cif file (from database like http://www.crystallography.net/) for the molecule in question.
If you place the three molecules in some configuration and then relax them, there is a fair possibility that you may end up in an optimized structure of some sorts.
However, that will simply be optimization of structure in the local potential energy well of the struture. It need not correspond to some physically found solid state crystal structure of that molecule.
So, your best bet is procuring the correct cif file, either from available database, or by taking help from a crystallographer who could help you getting cif of the relevant molecule using XRD of the physical sample of that molecule.
Hi, Vaibhav! Thanks for your kind answer! Actually, I have downloaded the cif file from RSC Protein Data Bank. I opened it with txt editing software. I can't find any lattice information. I also tried many software such as Mecury, VESTA and Jmol. Only Jmol can open it. I think there must be something wrong with the file. Could you help me to check the file? I attached it.
I downloaded cif file from the website as you suggested. That file is readable for many software. When I imported it to Material studio, I found only atoms without bond. What caused this problem? What is the unit of distance in MS?
1. Generally speaking CIF files could include the bonding or not. On the other hand, you can specify the bonding by deciding the distance between atoms.
2. The unit of MS is angstrom (Å, 10^-10 m).
The cif file in indeed incomplete. For one, I could not find information about its cell parameters, A, B, C, alpha, beta, gamma in the file. I too tried different softwares, but since the file itself if incomplete, I doubt if any others would help.
In that case, you could either consult a crystallographer on this, or try and locate a better cif.
Sorry I could not help you through this.
All the very best to you.
If crystal structures do not include bonding information, you can import them into Materials Studio and then use Build | Bonds to calculate bonds. You should check the bond orders are okay after you have calculated bonds.
If you are just adding atoms into the unit cell manually, you can use Build | Add Atoms to add unique atoms at specific positions. On the Options tab for this dialog, you can specify whether you are adding in fractional or cartesian coordinates.
To get the fractional coordinates option, you must have a 3D atomistic document in focus containing a crystal lattice (ie empty cell created from Build Crystal or imported).
I want to import a structure from txt file in material studio 2020 but am unable to do so. The file gets uploaded but coordinates are opening rather than 3D structure..can anyone guide?
I want to import a structure from txt file in material studio 2020 but am unable to do so. The file gets uploaded but coordinates are opening rather than 3D structure..can anyone guide?
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biochemical Techniques
- Analytical Chemistry
- pH