Questions tagged [cif]

For questions about the use of Crystallographic Information File – file format used in structural sciences.

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11
votes
2answers
224 views

How to sort a supercell for a molecular crystal?

I am trying to build a supercell of the following (below) molecular crystal from its .cif file. How do I sort a supercell here according to each molecule in the supercell? I'm not tethered to a ...
5
votes
1answer
104 views

ASE: why do I get warnings about “monoclinic” and “orthorhombic” not being interpreted?

I am trying to use ASE (Atomic Simulation Environment) to build a supercell of some molecular crystals and then output the result to a file with the atoms given in a specified order for each molecule, ...
8
votes
2answers
176 views

Extracting the coordinates of a super cell in Vesta or Avogadro

I am trying to use a program such as Vesta or Avogadro to build a super cell from a .cif file for a molecular crystal. In neither program can I seem to figure out how to order the output of the ...
5
votes
1answer
102 views

How to resolve the cif2cell TypeError?

I have encountered an error using cif2cell while covering a CIF file from COD to quantum ESPRESSO format. The error is as follows. command typed: $cif2cell crystal.cif -p quantum-espresso -o crystal....
11
votes
6answers
1k views

How do I extract a molecular structure from a CIF file?

When I open a CIF file of a crystal structure in a typical molecular editor like Avogadro, then I just see a few symmetry-unique atoms scattered around the unit cell. But I don't see the full molecule ...
13
votes
3answers
523 views

9 x 9 x 9 periodic xyz file to cif file format

I have a 9 x 9 x 9 periodic crystal structure in .xyz format and I would like to change it to .cif file format. Does anyone know how to convert the file? (e.g. 9 x 9 x 9 to unit cell then cif)
16
votes
2answers
99 views

Is it necessary to optimize structures obtained from a cif file?

Crystallographic Information Files (CIF) are, in general, obtained from experimental measurements. Since the information originated from real samples, is it mandatory to relax the structure in order ...
16
votes
1answer
152 views

What are the differences between crystal structure file formats like CIF, XYZ, PDB etc.?

We come across many file formats like CIF, XYZ, PDB, INS, cc1, p1, POSCAR, FDF, struct etc. Why do we have so many file formats to store crystal structure information? Are they redundant? Can someone ...
11
votes
2answers
134 views

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

All the tutorials I see online for creating a molecular model are either for small molecules or for crystal systems. I can't seem to figure out how to create a model for a core-shell nanoparticle. Is ...
17
votes
2answers
241 views

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

I tried to recover a .CIF file (Crystallographic Information File) with the crystal structure for the compound discussed in a paper by Reuter et. al.[1], strontium hydroxide octahydrate - $\ce{Sr(OH)2·...