How to citate a crystallographic software

last update: 24 Jan., 2023

A journal references for crystallographic software:


L. J. Barbour,
X-Seed 4: updates to a program for small-molecule supramolecular crystallography.
J. Appl. Cryst. 53, (2020) 1141-1146.


L. J. Barbour,
X-Seed – A Software Tool for Supramolecular Crystallography
J. Supramol. Chem., 1, (2001) 189-191.

About the combination of crystalography and art:

Atwood, J.L., Barbour, L.J.,
Molecular Graphics:  From Science to Art
Crystal Growth & Design 3(1), (2003), 3-8.


Persistence of Vision Pty. Ltd. (2004). Persistence of Vision (TM) Raytracer. Persistence of Vision Pty. Ltd., Williamstown, Victoria, Australia.


C. B. Hübschle, G. M. Sheldrick and B. Dittrich,
ShelXle: a Qt graphical user interface for SHELXL
J. Appl. Cryst., 44, (2011) 1281-1284.


O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann, OLEX2: A complete structure solution, refinement and analysis program. J. Appl. Cryst., 42, (2009) 339-341.


A program to compute non-spherical atomic scattering factors for organic crystals.

P. Kumar, B. Gruza, S. A. Bojarowski and P. M. Dominiak. Extension of the transferable aspherical pseudoatom data bank for the comparison of molecular electrostatic potentials in structure–activity studies. Acta Cryst. A75, (2019) 398-408.

Chodkiewicz, M. L., Migacz, S., Rudnicki, W., Makal, A., Kalinowski, J. A., Moriarty, N. W., Grosse-Kunstleve, R. W., Afonine, P. V., Adams, P. D. and Dominiak, P. M. DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs. J. Appl. Cryst. 51, (2018) 193-199.


L. J. Farrugia, WinGX and ORTEP for Windows: an update. J. Appl. Cryst.,45, (2012) 849-854.


V. Petricek, M. Dusek, and L. Palatinus,
Crystallographic Computing System JANA2006: General features
Z. Kristallogr. 229, (2014) 345-352.

Other references (for special topics):

Petricek, V., Eigner, V., Dusek, M. & Cejchan, A.
Discontinuous modulation functions and their application for analysis of modulated structures with the computing system JANA2006
Z. Kristallogr. 231(5), (2016). 301-312.
DOI: 10.1515/zkri-2015-1913

Petricek, V., Dusek, M. & Plasil, J.
Crystallographic computing system Jana2006: solution and refinement of twinned structures
Z. Kristallogr. 231(10), (2016) 583-599.
DOI: 10.1515/zkri-2016-1956


G. M. Sheldrick
Phase annealing in SHELX-90: direct methods for larger structures
Acta Cryst., A46, (1990) 467-473.


G. M. Sheldrick,
Crystal structure refinement with SHELXL
Acta Cryst., C71, (2015) 3-8. (Open Access)


George M. Sheldrick, A short history of SHELX Acta Cryst., A64, (2008) 112-122.


G. M. Sheldrick SHELXT – Integrated space-group and crystal-structure determination Acta Cryst., A71, (2015) 3-8.

EXPO 2013, EXPO 2014

A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni, R. Rizzi, N. Corriero and A. Falcicchio, EXPO2013: a kit of tools for phasing crystal structures from powder data,
J. Appl. Cryst. 46, (2013) 1231-1235.

EXPO 2014

Altomare, Angela & Ciriaco, Fulvio & Cuocci, Corrado & Falcicchio, Aurelia & Fanelli, Flavio. Combined powder X-ray diffraction data and quantum-chemical calculations in EXPO2014. Powder Diffraction 32 (2017) 1-6.


A. Thorn and G. M. Sheldrick ANODE: anomalous and heavy-atom density calculation J. Appl. Cryst., A44, (2011) 1285-1287.

Superflip (also implemented in JANA2006, WinGX, Crystals, FullProf)

L. Palatinus and G. Chapuis, SUPERFLIP – a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions, J. Appl. Cryst., 40, (2007) 786-790.

Charge-flipping algorithm (CFA)

L. Palatinus, The charge-flipping algorithm in crystallography Acta Cryst., B69, (2013) 1-16.


A. L. Spek, Structure validation in chemical crystallography Acta Cryst., D65, (2009) 148-155.

SQUEEZE (Platon)

A. L. Spek, PLATON SQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors Acta Cryst., C71, (2015) 9-18.

Comment: Platon Squeeze is a tool, that determines the contribution of a disordered solvent or ion to the calculated structure factors.



Rigaku Oxford Diffraction.
Rigaku Corporation, Tokyo, Japan, 2019.


Rigaku Oxford Diffraction;
CrysAlisPro Software System;
Rigaku Corporation: Oxford, UK, 29 June 2015.

e.g. (old):
Oxford Diffraction.
CrysAlis Version 1.171.13 beta (release 14.11.2003 CrysAlis171 VC++).
Oxford Diffraction, UK, 2003.


Strategy of X-ray measurements for High Pressure experiments

A. Budzianowski and A. Katrusiak, Book Section: High-Pressure Crystallographic Experiments with a CCD-Detector in High-Pressure Crystallography NATO Science Series 140, (2004), 101-112. Eds.: A. Katrusiak, P. McMillan. Kluwer Academic Publishers, Springer, the Netherlands, Dordrecht (2004), 101-112.

ISBN: 978-1-4020-1954-8


SIR2014  or SIR2019

M.C. Burla, R. Caliandro, B. Carrozzini, G. L. Cascarano, C. Cuocci, C. Giacovazzo, M. Mallamo, A. Mazzone and G. Polidori
Crystal structure determination and refinement via SIR2014,
J. Appl. Cryst. 48, (2015) 306–309.


M. C. Burla, R. Caliandro, M. Camalli, B. Carrozzini, G. L. Cascarano, L. De Caro, C. Giacovazzo, G. Polidori and R. Spagna,
J. Appl. Cryst., 38,  (2005) 381-388.

Oscail 2016

P. McArdle,
Oscail, a program package for small-molecule single-crystal crystallography with crystal morphology prediction and molecular modelling
J. Appl. Cryst. 50, (2017) 320-326.


K. Momma and F. Izumi,
VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data.
J. Appl. Crystallogr., 44, (2011) 1272-1276.


C. F. Macrae, I. Sovago, S. J. Cottrell, P. T. A. Galek, P. McCabe, E. Pidcock, M. Platings, G. P. Shields, J. S. Stevens, M. Towler and P. A. Wood,
Mercury 4.0: from visualization to analysis, design and prediction
J. Appl. Cryst. 53, 226-235, 2020
[DOI: 10.1107/S1600576719014092]

Previous publications highlighting new Mercury functionality that may be of interest include:

C. F. Macrae, I. J. Bruno, J. A. Chisholm, P. R. Edgington, P. McCabe, E. Pidcock, L. Rodriguez-Monge, R. Taylor, J. van de Streek and P. A. Wood,
Mercury CSD 2.0 – New Features for the Visualization and Investigation of Crystal Structures
J. Appl. Cryst., 41, 466-470, 2008
[DOI: 10.1107/S0021889807067908]

C. F. Macrae, P. R. Edgington, P. McCabe, E. Pidcock, G. P. Shields, R. Taylor, M. Towler and J. van de Streek,
Mercury: visualization and analysis of crystal structures
J. Appl. Cryst., 39, 453-457, 2006
[DOI: 10.1107/S002188980600731X]

I. J. Bruno, J. C. Cole, P. R. Edgington, M. K. Kessler, C. F. Macrae, P. McCabe, J. Pearson and R. Taylor,
New software for searching the Cambridge Structural Database and visualising crystal structures
Acta Cryst., B58, 389-397, 2002
[DOI: 10.1107/S0108768102003324]

R. Taylor and C. F. Macrae,
Rules governing the crystal packing of mono- and di-alcohols
Acta Cryst., B57, 815-827, 2001
[DOI: 10.1107/S0108768102003324]


Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D., Spackman, M. A.
CrystalExplorer: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals

J. Appl. Cryst. 54, (2021) 1006-1011.

CrystalExplorer – Fingerprint plots

M. A. Spackman & J. J. McKinnon,
Fingerprinting intermolecular interactions in molecular crystals
CrystEngComm 4, (2002) 378-392.

CrystalExplorer – CE Model Interaction Energies

Mackenzie, Campbell F. and Spackman, Peter R. and Jayatilaka, Dylan and Spackman, Mark A.
CrystalExplorer model energies and energy frameworks: extension to metal coordination compounds, organic salts, solvates and open-shell systems
4, (2017) 575-587.

Diamond – Crystal and Molecular Structure Visualization (Crystal Impact)

Publications about and reviews of Diamond can be found here:

  • J. Res. Natl. Inst. Stand. Technol. 101 (1996) 221.
  • J. Appl. Cryst. 32, (1999) 1028-1029.
  • Nachr. Chem. Techn. Lab. 12, (1999) 1437-1438.
  • Scientific Computing World 57, (2001) 28-30.
  • Scientific Computing World 63, (2002) 19-21.

Autostereogram – almost normal flat image that contains info to see it see also with depth perception (like 3D).

Katrusiak, A.
Crystallographic autostereograms
J Mol Graph Model. 19(3-4), 2001, 363−367.


Powder diffraction data:


Altomare, A., Corriero, N., Cuocci, C., Falcicchio, A., Moliterni, A., Rizzi, R.
QUALX2.0: a qualitative phase analysis software using the freely available database POW_COD
J. Appl. Cryst. 48, (2015) 598-603.


A. Altomare, C. Cuocci, C. Giacovazzo, A. Moliterni and R. Rizzi,
QUALX: a computer program for qualitative analysis using powder diffraction data
J. Appl. Cryst., 41, (2008) 815-817.

Crystal Sleuth

T. A. Laetsch, R. T. Downs,
Software for identification and refinement of cell parameters from powder diffraction data of minerals using the RRUFF Project and American Mineralogist Crystal Structure Databases.
Program and Abstracts of the 19th General Meeting of the International Mineralogical Association in Kobe, Japan (2006). P08-25


M. Wojdyr, Fityk: a general-purpose peak fitting program J. Appl. Cryst., 43, (2010) 1126-1128.

Comment: curve fitting, Pawley refinement


Oishi R., Yonemura M., Nishimaki Y., Torii S., Hoshikawa A., Ishigaki T., Morishima T., Mori K., Kamiyama T.
Rietveld analysis software for J-PARC,
Nuclear Instruments and Methods A600, (2009) 94–96.

Oishi-Tomiyasu R., Yonemura M., Morishima T., Hoshikawa A., Torii S., Ishigaki T., Kamiyama T.
Application of matrix decomposition algorithms for singular matrices to the Pawley method in Z-Rietveld
J. Appl. Cryst. 45, (2012) 299–308

Endeavour – Structure Solution from Powder Diffraction

H. Putz, J.C. Schoen, M. Jansen,
Combined Method for „Ab Initio” Structure Solution from Powder Diffraction Data,
J. Appl. Cryst. 32, (1999)864-870.


Juan Rodríguez-Carvajal,
Recent advances in magnetic structure determination by neutron powder diffraction,
Physica B: Condensed Matter 192(1–2), (1993) 55-69.

The complete program and documentation can be obtained in


Toby, B. H., & Von Dreele, R. B.
GSAS-II: the genesis of a modern open-source all purpose crystallography software package”.
J. Appl. Cryst. 46(2), (2013). 544-549.


A.C. Larson and R.B. Von Dreele,
General Structure Analysis System (GSAS),
Los Alamos National Laboratory Report LAUR 86-748 (2004).


Coelho, Alan A.,
TOPAS and TOPAS-Academic: an optimization program integrating computer algebra and  crystallographic objects written in C++,
Journal of Applied Crystallography 51(1) (2018), 210-218.


A. Coelho,
TOPAS Academic, Version 4.1. Coelho Software, (2007) Brisbane. A. Coelho, TOPAS Academic Technical Reference. Coelho Software, (2012) Brisbane.

Charge-flipping algorithm (CFA) in TOPAS

G. Oszlányi and A. Sütő,
Ab initio structure solution by charge flipping Acta Cryst., A60, (2004) 134–141.

A. A. Coelho,
A charge-flipping algorithm incorporating the tangent formula for solving difficult structures
Acta Cryst., A63, (2007) 400-406.


EVA 14, DIFFRACplus BASIC Evaluation Package, Bruker AXS User’s Manual, Release 2008


AbsorbDX 1.1.4, DIFFRACplus BASIC Evaluation Package, Bruker AXS User’s Manual, Release 2008


Bortolotti M., Lutterotti L., Lonardelli I.
ReX: a computer program for structural analysis using powder diffraction data.
J. Appl. Cryst. 42, (2009) 538-539.


Bortolotti M., Lonardelli I.,
ReX.Cell: a user-friendly program for powder diffraction indexing
J. Appl. Cryst. 46, (2013) 259-261.

Also, don’t forget to report the particular indexing engine used, e.g.:


Boultif A., Louër, D.
Powder pattern indexing with the dichotomy method,
J. Appl. Cryst. 37, (2004) 724-731,


Visser J. W.,
A fully automatic program for finding the unit cell from powder data,

J. Appl. Cryst. 2, (1969). 89-95,


Werner P.-E., Eriksson L., Westdahl, M.
TREOR, a semi-exhaustive trial-and-error powder indexing program for all symmetries,
J. Appl. Cryst. 18, (1985) 367-370,


A. Le Bail,
Monte Carlo Indexing with McMaille
Powder Diffraction 19 (2004) 249-254.

 X-Cell (Materials Studio)

Neumann, Marcus A.
X-Cell: a novel indexing algorithm for routine tasks and difficult cases,
Journal of Applied Crystallography 36(2): (2003) 356–365.


Kraus, Werner & Nolze, Gert
PowderCell 2.0 for Windows
Powder Diffraction 13, (1998) 256-259.


The program to analyse diffraction spectra and obtain crystal structures, quantity and microstructure of phases along with the texture and residual stresses.

L. Lutterotti,
Total pattern fitting for the combined size-strain-stress-texture determination in thin film diffraction,
Nuclear Inst. and Methods in Physics Research, B, 268, 334-340, 2010.

L. Lutterotti, M. Bortolotti, G. Ischia, I. Lonardelli and H.-R. Wenk,
Rietveld texture analysis from diffraction images,
Z. Kristallogr., Suppl. 26, 125-130, 2007.

L. Lutterotti, D. Chateigner, S. Ferrari and J. Ricote,
Texture, Residual Stress and Structural Analysis of Thin Films using a Combined X-Ray Analysis, Thin Solid Films, 450, 34-41, 2004.

L. Lutterotti, S. Matthies, H.-R. Wenk, A.J. Schultz and J. Richardson,
Combined texture and structure analysis of deformed limestone from neutron diffraction spectra,
J. Appl. Phys., 81[2], 594-600, 1997.

Analysis examples:

L. Lutterotti, P. Polonioli, P. G. Orsini and M. Ferrari,
Stress and texture analysis of zirconia coatings by XRD total pattern fitting, in ASME Materials and Design Technology 1994, Ed. T. J. Kozik, ASME, 15-20, 1994.

L. Lutterotti, S. Matthies, H.-R. Wenk, A.J. Schultz and J. Richardson,
Texture and structure analysis of deformed limestone from neutron diffraction spectra,
J. Appl. Phys., 81[2], 594-600, (1997).

D. Chateigner, L. Lutterotti & T. Hansen,
Quantitative phase and texture analysis of ceramic matrix composites,
ILL Annual Report 97, 1998.

Microstructure and Rietveld

L. Lutterotti & P. Scardi,
Simultaneous Structure and Size-Strain Refinement by the Rietveld Method,
J. Appl. Cryst. (1990), 23, 246-252.

L. Lutterotti and S. Gialanella,
X-ray diffraction characterization of heavily deformed metallic specimens,
Acta Materialia, 46[1], 101-110, (1998).

P. Scardi, L. Lutterotti & P. Maistrelli,
Experimental Determination of the Instrumental Broadening in the Bragg-Brentano Geometry. Powder Diffraction., 9 (3), pp.180-186, 1994.


H.-R. Wenk, S. Matthies and L. Lutterotti,
Texture analysis from diffraction spectra,
Mater. Sci. Forum, 157-162, 473-480, 1994.

M. Ferrari, L. Lutterotti, S. Matthies, P. Polonioli, H. -R. Wenk,
New opportunities in the texture and stress field by the whole pattern analysis,
Mat. Sci. Forum, vols 228-231, pp. 83-88, (1996).

S. Matthies, L. Lutterotti and H. -R. Wenk,
Progress in combining Rietveld and QTA Algorithms on Advanced Level,
Presented at ICOTOM 11, China, September 1996.

S. Matthies, L. Lutterotti, H. -R. Wenk,
Advances in Texture Analysis from Diffraction Spectra,
J. Appl. Cryst., 30, 31-42, (1997).


M. Ferrari and L. Lutterotti,
Method for the simultaneous determination of anisotropic residual stresses and texture by X-ray diffraction,
J. Appl. Phys., 76 (11), 7246-55, 1994.

Analysis and Visualisation of 2D Images:


A. P. Hammersley
FIT2D: a multi-purpose data reduction, analysis and visualization program
J. Appl. Cryst. 49, (2016) 646-652.

LAMP – Large Array Manipulation Program (ILL)

D. Richard, M. Ferrand and G.J. Kearley,
Analysis and Visualisation of Neutron-Scattering Data
J. Neutron Research 4(1-4), (1996) 33-39.
DOI: 10.1080/10238169608200065

Esmeralda Laue Suite

Rodriguez-Carvajal, J., Fuentes-Montero, L., Cermak, P.,
to be published. See the web page

Fuentes-Montero, Luis & Cermak, Petr & Rodríguez-Carvajal, Juan & Filhol, Alain (2015)
The Esmeralda suite for Laue diffraction data treatment.


Data conversion:


Allouche, A.-R.
Gabedit—A graphical user interface for computational chemistry softwares.
J. Comput. Chem. 32,  (2011) 174-182.


Free cross-platform molecular editor – Avogadro

  • Avogadro: an open-source molecular builder and visualization tool. Version 1.XX.
  • Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek and Geoffrey R Hutchison;
    Avogadro: An advanced semantic chemical editor, visualization, and analysis platform Journal of Cheminformatics 2012, 4:17.

Data bases:

COD – Crystallography Open Database

Vaitkus, A., Merkys, A. & Grazulis, S.
Validation of the Crystallography Open Database using the Crystallographic Information Framework
J. Appl. Cryst. 54, (2021), 661-672.

Quirós, M., Gražulis, S., Girdzijauskaitė, S., Merkys, A. & Vaitkus, A.
Using SMILES strings for the description of chemical connectivity in the Crystallography Open Database
J Cheminform 10, 23 (2018).

Merkys, A., Vaitkus, A., Butkus, J., Okulič-Kazarinas, M., Kairys, V. & Gražulis, S.
COD::CIF::Parser: an error-correcting CIF parser for the Perl language.
J. Appl. Cryst. 49 (2016).

Gražulis, S., Merkys, A., Vaitkus, A. & Okulič-Kazarinas, M.
Computing stoichiometric molecular composition from crystal structures.
J. Appl. Cryst. 48, (2015) 85-91.

Gražulis, S., Daškevič, A., Merkys, A., Chateigner, D., Lutterotti, L., Quirós, M., Serebryanaya, N. R., Moeck, P., Downs, R. T. & LeBail, A.
Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration.
Nucleic Acids Research 40, (2012) D420-D427.

Gražulis, S., Chateigner, D., Downs, R. T., Yokochi, A. T., Quiros, M., Lutterotti, L., Manakova, E., Butkus, J., Moeck, P. & Le Bail, A.
Crystallography Open Database – an open-access collection of crystal structures.
J. Appl. Cryst. 42, (2009) 726-729.

Downs, R. T. & Hall-Wallace, M.,
The American Mineralogist Crystal Structure Database.
American Mineralogist 88, (2003) 247-250.

PCOD – Predicted Crystallography Open Database

Le Bail
Inorganic structure prediction with GRINSP.
J. Appl. Cryst. 38, (2005) 389-395

The Open Chemistry Database, OChemDb

Altomare, A., Corriero, N., Cuocci, C., Falcicchio, A., Moliterni, A., Rizzi, R.
OChemDb: the free on-line Open Chemistry Database portal for searching and analysing crystal structure information.
J. Appl. Cryst. 51, (2018) 1229-1236.

The American Mineralogist Crystal Structure Database

Downs, R.T. and Hall-Wallace, M.
The American Mineralogist Crystal Structure Database.
American Mineralogist 88, (2003) 247-250.

Mineralogy Database

at is a collection of minerals with crystallographic information.

The Cambridge Crystallographic Data Centre (CCDC)

at is for organic, metal-organic, and inorganic compounds, including extended molecular solids and also powder data where a constrained refinement has been used.

International Centre for Diffraction Data (ICDD)

at collect powder diffraction data without atomic coordinates.

Protein Data Bank (PDB)

at accumulate polypeptides and polysaccharides that contain more than 24 units.

Incommensurate Structures Database (ICSDB)

at is for incommensurate, modulated and composite structures.

Nucleic Acids Data Bank

at collects oligonucleotides.

CCDC ConQuest

I. J. Bruno, J. C. Cole, P. R. Edgington, M. Kessler, C. F. Macrae, P. McCabe, J. Pearson and R. Taylor,
New software for searching the Cambridge Structural Database and visualising crystal structures
Acta Cryst., B58 (2002), 389-397. DOI: 10.1107/S0108768102003324.



Wyckoff Positions

Aroyo, Mois Ilia, Perez-Mato, Juan Manuel, Capillas, Cesar, Kroumova, Eli, Ivantchev, Svetoslav, Madariaga, Gotzon, Kirov, Asen and Wondratschek, Hans.
Bilbao Crystallographic Server: I. Databases and crystallographic computing programs.
Zeitschrift für Kristallographie – Crystalline Materials, 221(1), (2006),  15-27.

Other Useful Citations: link

Link to High-Resolution Space Group Diagrams and Tables

(IUCr) Crystallographic resources


Barbour, L. J.
EwaldSphere: an interactive approach to teaching the Ewald sphere construction
J. Appl. Cryst. 51, (2018) 1734-1738.

Friedel’s pairs

Bijvoet, J. M., Peerdeman, A. F. and van Bommel, A. J.
Determination of the absolute configuration of optically active compounds by means of X-rays Nature (London), 168, (1951) 271–272.

Non-crystallographic calculations:


Giuseppe M. J. Barca, Colleen Bertoni, Laura Carrington, Dipayan Datta, Nuwan De Silva, J. Emiliano Deustua, Dmitri G. Fedorov, Jeffrey R. Gour, Anastasia O. Gunina, Emilie Guidez, Taylor Harville, Stephan Irle, Joe Ivanic, Karol Kowalski, Sarom S. Leang, Hui Li, Wei Li, Jesse J. Lutz, Ilias Magoulas, Joani Mato, Vladimir Mironov, Hiroya Nakata, Buu Q. Pham, Piotr Piecuch, David Poole, Spencer R. Pruitt, Alistair P. Rendell, Luke B. Roskop, Klaus Ruedenberg, Tosaporn Sattasathuchana, Michael W. Schmidt, Jun Shen, Lyudmila Slipchenko, Masha Sosonkina, Vaibhav Sundriyal, Ananta Tiwari, Jorge L. Galvez Vallejo, Bryce Westheimer, Marta Włoch, Peng Xu, Federico Zahariev, and Mark S. Gordon
Recent developments in the general atomic and molecular electronic structure system
J. Chem. Phys. 152, (2020) 154102


Humphrey, W., Dalke, A. and Schulten, K.,
VMD -Visual Molecular Dynamics,
J. Molecular Graphics, 1996, vol. 14, pp. 33-38.