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Questions tagged [crystallographic-information-file]

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

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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 ...
Thomas's user avatar
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19 votes
2 answers
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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

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·...
ksousa's user avatar
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17 votes
2 answers
369 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 ...
Anibal Bezerra's user avatar
14 votes
7 answers
4k 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 ...
Felix's user avatar
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13 votes
2 answers
581 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 ...
jboy's user avatar
  • 1,151
13 votes
3 answers
2k 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)
DGKang's user avatar
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13 votes
1 answer
2k views

Extracting molecular structure from CIF file using VESTA or Mercury

I am trying to extract XYZ coordinates from a CIF file for a molecule to use in DFT calculations. I have Mercury and Vesta installed on my computer. Whenever I open the files, I get the following ...
Collodial_machine 's user avatar
12 votes
2 answers
516 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 ...
user avatar
9 votes
0 answers
127 views

Is there a script that will suggest (hkl) indices based on distances in an electron diffraction pattern for a known crystal structure? [closed]

I am looking for a script (preferably in Python) that will suggest (hkl) indices based on distances in an electron diffraction pattern. The crystal structure is known,i.e. I have the CIF file and know ...
Anya's user avatar
  • 179
8 votes
2 answers
888 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 ...
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8 votes
1 answer
552 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....
Anoop A Nair's user avatar
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7 votes
2 answers
469 views

Change cif file into vesta format

I have 100 .cif files. I want to convert them all to .vesta files through vesta software (https://jp-minerals.org/vesta/en/download.html). I know I can choose them one by one and convert them. Is ...
Sanu's user avatar
  • 71
7 votes
2 answers
849 views

How to generate the SMILES for .cif files correctly and how do I generate .pkl or .pickle file out of these SMILES

I used openbabel to convert the .cif files to .smi. Here are parts of the .smi corresponding to two .cif files (I have many .cif files): ...
Rose Vanilla's user avatar
7 votes
2 answers
269 views

How can I make a CIF file for Monoclinic MoO2?

A CIF file of Monoclinic $\ce{MoO2}$ is not available in the Crystallography Open Database website. How can I make it myself or find it elsewhere?
user4106's user avatar
  • 121
6 votes
1 answer
511 views

How are the simulated powder diffraction patterns calculated in CCDC Mercury?

From my understanding, programs like CCDC Mercury and VESTA are able to extract some information from imported .CIF files of molecules but then complete calculations to output a simulated X-ray ...
John's user avatar
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6 votes
0 answers
499 views

How to create a CIF using VESTA? [closed]

I am looking into double perovskite materials. One of the possible materials is $\ce{Cs4CuSb2Cl12}$. Now, although there are a few papers which have done ab intio calculations but none of the common ...
Parmeet Singh EP 066's user avatar
5 votes
1 answer
811 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, ...
user avatar
5 votes
1 answer
2k views

1T and 1H CIF file for MoS2

On the COD website, only 2-layer hexagonal (2H) and 3-layer orthorhombic (3R) $\ce{MoS2}$ are available. I can't find the 1-layer tetragonal (1T) and 1H CIF for $\ce{MoS2}$. Where can I find them, or ...
user4106's user avatar
  • 121
5 votes
1 answer
162 views

Can a CHGCAR file be converted into a CIF file?

A .cif file can be used for multiple purposes and is a more generic format to store atomic data.
Pranoy Ray's user avatar
  • 1,635
5 votes
1 answer
415 views

Which applications can convert multiple CIF files to multiple XYZ files all at once

I have tried a bunch of apps such as Mercury, OpenLabel but they cannot convert CIF files to XYZ files in bulk. I am also thinking of doing it in Python but just want to know if there's an app for ...
Rose Vanilla's user avatar
4 votes
1 answer
68 views

Isotropy of Pymatgen Structures

I'm using pymatgen and have a host of structure objects (generated from cif files). How can I judge if the structure is isotropic or not? I took a look at the options associated with structure objects ...
R Walser's user avatar
  • 367
4 votes
1 answer
614 views

What's the appropriate method to create a supercell for Quantum ESPRESSO?

I created a CIF file using the experimental parameters of my material, then I used it to create my input file for the unit cell using Cif2Cell. After that, I ...
Camilla's user avatar
  • 2,169
4 votes
1 answer
173 views

cif2cell command error

I am having the following error while converting the CIF file of a hypothetical crystal into an input file for Quantum espresso. ...
Mohammad Bakhsh's user avatar
3 votes
1 answer
129 views

How to generate the remaining sites in a cubic lattice from a given POSCAR/cif in Python?

For example, I intend to generate the remaining sites of the Cr cubic lattice but the POSCAR file provides limited info on the number of atoms present as shown below. Is there a way to implement this ...
Pranoy Ray's user avatar
  • 1,635
3 votes
1 answer
74 views

Do I have to use Rwp, RI, Rf and atomic displacement parameter B to create a CIF file?

I want to create the CIF file of CuI using VESTA software.I used the following parameters to create my CIF : space group, lattice parameter, the angles (alpha, beta and gamma), atomic positions of Cu ...
Camilla's user avatar
  • 2,169
3 votes
1 answer
80 views

How to generate Quantum ESPRESSO input file for a system containing amino acid residues and a metal ion?

I want to optimise a system containing few amino acid residues (residues in active site of an enzyme) with a metal ion, in order to show a proposed mechanism is correct for the enzyme inhibition. For ...
PriZarah's user avatar
  • 409
2 votes
1 answer
117 views

How to make a super cell for molecular crystal with PBC

I am trying to build a supercell for molecular crystals from a .cif file. With the ASE package, the supercell has the perfect PBC, but the atom sequence is very random and might be difficult to match ...
Pradip Si's user avatar
1 vote
1 answer
56 views
+50

CIF file for Methyl Acrylate (MA) and how does the chain of a few MA look like?

The information of Methyl Acrylate (MA) can be seen from this Link. If MA is somehow crystalizes and bonded as a chain (for example, 5 units of MA is bonded together forming a chain), what will be the ...
Sak's user avatar
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1 vote
0 answers
9 views

checkcif and PLATON ellipsoid plot: crystall structure does not look right

When I open my CIF file in VESTA it looks ok. When I upload it to https://checkcif.iucr.org/, the ellipsoid plot produced by PLATON does not look right. The unit cell of the supercell is not fully ...
freude's user avatar
  • 392