International
Tables for
Crystallography
Volume B
Reciprocal space
Edited by U. Shmueli

International Tables for Crystallography (2010). Vol. B, ch. 3.3, pp. 442-445

Section 3.3.4. Graphics software for the display of small and medium-sized molecules

L. M. D. Cranswickb

3.3.4. Graphics software for the display of small and medium-sized molecules

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3.3.4.1. Introduction

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In the age of the Internet, a wide variety of software can be easily obtained for the display of small and medium-sized molecules. An obvious question to ask is `which software is the best?'. It can be `best' to try all the relevant available software quickly before settling on two to three programs that are found to be most suitable. Not relying on just a single program can be important for visual and numeric cross validation of the resulting structural plot, as bugs (if present) can be quite subtle in their effect, but moderately easy to find by comparing plots made by different programs.

Most software can import crystallographic data in some format. The IUCr CIF format [see International Tables for Crystallography Volume G (2005[link])] is slowly becoming a standard in this regard, displacing the single-crystal SHELX INS format, which has been a de-facto standard file format for much crystallographic data exchange. Entering crystallographic data by hand is slow and often introduces errors via typographical mistakes. Such mistakes can be minimized by importing structures using a known file type, or reformatting using a text editor or spreadsheet program into a known file type. A variety of software programs can be used for translating crystallographic structure files; however, the output (especially the handling of the symmetry operators and the space group) should be carefully checked. The CCP14 website (Cockroft & Stephenson, 2005[link]) lists a variety of programs that can be used for this, of which a specialist program is Cryscon (Dowty, 2005[link]).

3.3.4.2. Types of crystal structure display and functionality

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The following information was current at the time of writing, but most software is continually changing with the insertion of new features. Thus occasional checks for updated functionality can be useful. Most software distributions include an `updates' file containing new features and bug fixes. Detailed information on the software referred to in this section, including functionality, authorship, source and availability, is given in Tables 3.3.4.1[link] and 3.3.4.2[link].

Table 3.3.4.1| top | pdf |
Functionality of software for crystal structure display

ProgramBall and stickADPsMSDAPolyhedral displayCartesian coordinatesComparison/overlay of multiple structuresExtended structures/topology analysisMagnetic structuresIncommensurate structures
ATOMS Yes Yes   Yes Yes     Yes  
Balls&Sticks Yes     Yes          
BALSAC Yes       Yes        
Cameron Yes Yes              
CaRIne Yes     Yes Yes        
Crystallographica Yes Yes   Yes          
CrystalMaker Yes     Yes Yes     Yes  
Crystal Studio Yes Yes   Yes Yes        
CrystMol Yes Yes     Yes Yes      
Diamond Yes Yes   Yes Yes     Yes  
DrawXTL Yes Yes   Yes       Yes  
FpStudio Yes Yes           Yes Yes
GRETEP Yes Yes         Yes    
Mercury Yes       Yes        
MolXtl Yes Yes     Yes        
OLEX Yes       Yes   Yes    
ORTEP-III Yes Yes              
ORTEP-3 for Windows Yes Yes Yes   Yes        
ORTEX/Oscail X Yes Yes              
PEANUT Yes Yes Yes            
Platon/Pluton Yes Yes     Yes        
PowderCell Yes                
PRJMS Yes               Yes
SCHAKAL Yes       Yes        
STRUPLO Yes     Yes          
STRUPLO for Windows       Yes Yes        
STRUVIR       Yes          
VENUS Yes Yes   Yes Yes     Yes  
XmLmctep Yes Yes              
X-Seed Yes Yes     Yes        
Xtal-3D Yes Yes   Yes       Yes  
XtalDraw Yes Yes   Yes          

Table 3.3.4.2| top | pdf |
Availability of software for crystal structure display

ProgramCompany or contact personContact and/or web addressReferenceStatus
ATOMS Shape Software 521 Hidden Valley Road, Kingsport, TN 37663, USA. http://www.shapesoftware.com/   Commercial
Balls&Sticks Tadashi Ozawa http://www.toycrate.org/ [1] Freeware
BALSAC Klaus Hermann Fritz-Haber-Institut der MPG, Berlin. http://w3.rz-berlin.mpg.de/~hermann/hermann/balpam.html [Copyright (1991–2004) Klaus Hermann. All rights reserved.]   Commercial
Cameron David Watkin http://www.xtl.ox.ac.uk/crystals.html [2] Freeware
CaRIne ESM Software http://pro.wanadoo.fr/carine.crystallography/ [Copyright (1989–2005) C. Boudias and D. Monceau.]   Commercial
Crystallographica Oxford Cryosystems Ltd http://www.crystallographica.co.uk/ [3] Commercial
CrystalMaker CrystalMaker Software Ltd 5 Begbroke Science Park, Sandy Lane, Yarnton, OX5 1PF, UK. http://www.crystalmaker.co.uk/ (CrystalMaker 6 for Mac OS X)   Commercial
Crystal Studio CrystalSoft & Crystal Systems Co. Ltd PO Box 7006, Wattle Park, VIC 3128, Australia. http://www.crystalsoftcorp.com/ [Copyright (1999–2005) Crystal Systems Co., Ltd]   Commercial
CrystMol David Duchamp 6209 Litchfield Lane, Kalamazoo, MI 49009–9159, USA. http://www.crystmol.com/   Commercial
Diamond Crystal Impact K. Brandenburg & H. Putz, Crystal Impact GbR, Postfach 1251, D-53002 Bonn, Germany. http://www.crystalimpact.com/   Commercial
DrawXTL Larry Finger http://lwfinger.net/drawxtl/ [4] Freeware
FpStudio Juan Rodriguez-Carvajal http://www.ill.fr/dif/soft/fp/ [5] Freeware
GRETEP Jean Laugier J. Laugier and B. Bochu, ENSP/Laboratoire des Matériaux et du Génie Physique, BP 46, 38042 Saint Martin d'Hères, France. http://www.ccp14.ac.uk/tutorial/lmgp/   Freeware
Mercury Cambridge Crystallographic Data Centre http://www.ccdc.cam.ac.uk/ [6] Freeware
MolXtl Dennis W. Bennett http://www.uwm.edu/Dept/Chemistry/molxtl/ [7] Freeware
OLEX Oleg Dolomanov http://www.ccp14.ac.uk/ccp/web-mirrors/lcells/olex_index.htm [8] Freeware
ORTEP-III Carroll Johnson http://www.ornl.gov/ortep/ortep.html [9] Freeware
ORTEP-3 for Windows Louis Farrugia http://www.chem.gla.ac.uk/~louis/software/ortep3/ [10] Freeware
ORTEX/Oscail X Patrick McArdle http://www.nuigalway.ie/cryst/software.htm [11], [12] Freeware
PEANUT Hans-Beat Bürgi Laboratorium für chemische und mineralogische Kristallographie, Universität Bern, Freiestrasse 3, CH-3012 Bern, Switzerland. E-mail: hans-beat.buergi@krist.unibe.ch [13] Freeware
Platon/Pluton Anthony Spek http://www.cryst.chem.uu.nl/platon/ [14], [15] Freeware
PowderCell Gert Nolze http://www.ccp14.ac.uk/ccp/web-mirrors/powdcell/a_v/v_1/powder/e_cell.html [16] Freeware
PRJMS Akiji Yamamoto http://quasi.nims.go.jp/yamamoto/ [17] Freeware
SCHAKAL Egbert Keller http://www.krist.uni-freiburg.de/ki/Mitarbeiter/Keller/schakal.html [18] Freeware
STRUPLO Reinhadt Fischer http://www.brass.uni-bremen.de/ [19] Freeware
STRUPLO for Windows Louis Farrugia http://www.chem.gla.ac.uk/~louis/software/struplo/ [19], [20] Freeware
STRUVIR Armel Le Bail http://www.cristal.org/vrml/struvir.html [19], [20] Freeware
VENUS Fujio Izumi http://homepage.mac.com/fujioizumi/visualization/VENUS.html [21], [22] Freeware
XmLmctep Alain Soyer http://www.lmcp.jussieu.fr/~soyer/Lmctep_en.html [23] Freeware
X-Seed Len Barbour http://x-seed.net/ [24], [25] Commercial
Xtal-3D Alan Hewat http://barns.ill.fr/dif/xtal-3d.html [26] Freeware
XtalDraw Bob Downs http://www.geo.arizona.edu/xtal/xtaldraw/xtaldraw.html [27] Freeware

References: [1] Ozawa & Kang (2004[link]); [2] Watkin et al. (1996[link]); [3] Siegrist (1997[link]); [4] Finger et al. (2007[link]); [5] Chapon & Rodriguez-Carvajal (2005[link]); [6] Bruno et al. (2002[link]); [7] Bennett (2004[link]); [8] Dolomanov et al. (2003[link]); [9] Burnett & Johnson (1996[link]); [10] Farrugia (1997[link]); [11] McArdle (1994[link]); [12] McArdle et al. (2004[link]); [13] Hummel, Hauser & Bürgi (1990[link]); [14] Spek (1998[link]); [15] Spek (2003[link]); [16] Kraus & Nolze (1996[link]); [17] Yamamoto (1982[link]); [18] Keller (1999[link]); [19] Fischer (1985[link]); [20] Le Bail (1996[link]); [21] Izumi & Dilanian (2002[link]); [22] Izumi (2004[link]); [23] Soyer (1993[link]); [24] Barbour (2001[link]); [25] Atwood & Barbour (2003[link]); [26] Hewat (2002[link]); [27] Downs & Hall-Wallace (2003[link]).

3.3.4.2.1. Ball and stick

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This is one of the most fundamental methods of displaying a crystal structure and almost all software supports this. The exceptions are STRUVIR and STRUPLO for Windows [a port of STRUVIR incorporating a graphical user interface (GUI)], which are both optimized for the polyhedral display of crystal structures.

3.3.4.2.2. Anisotropic displacement parameters

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A subset of the programs that display ball-and-stick structures can also display surfaces related to anisotropic displacement parameters (ADPs) (also known colloquially as `thermals', `anisotropic thermal ellipsoids' or `ORTEPS'). By default, most programs display the ellipsoid surfaces at a probability of 50% and normally allow this value to be changed to values between 1 and 99%. Programs that can draw ADPs include ATOMS, Cameron, Crystallographica, CrystalMaker, Crystal Studio, CrystMol, Diamond, DrawXTL, FpStudio, GRETEP, MolXtl, ORTEP-III, ORTEP-3 for Windows, ORTEX, PEANUT, Platon, VENUS, XmLmctep, X-Seed and XtalDraw.

3.3.4.2.3. Mean-square displacement amplitude

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When a more thorough investigation of the ADPs would be informative (Hummel, Raselli & Bürgi, 1990[link]), PEANUT can be used for plotting the mean-square displacement amplitude (MSDA), root-mean-square displacements (RMSDs) and difference surfaces. MSDA `peanuts' can be displayed where the ADPs are non-positive-definite and the ellipsoids cannot be drawn. ORTEP-3 for Windows also has an option for plotting MSDAs. Care should be taken to ensure the resulting display is correct.

3.3.4.2.4. Polyhedral display

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A method for understanding inorganic and intermetallic structures is the use of coordination polyhedra. The faces defined by the outer coordinated atoms generate a polyhedral object that is displayed instead of the individual atoms. This can aid in understanding the structures of polymeric inorganic materials involving both simple and complex tilt systems, and distorted coordination structures. Polyhedral display is provided by the programs ATOMS, Balls&Sticks, CaRIne, Crystallographica, CrystalMaker, Crystal Studio, Diamond, DrawXTL, STRUPLO, STRUPLO for Windows (a port of STRUVIR incorporating a GUI), STRUVIR, VENUS, Xtal-3D and XtalDraw. Nearly all the programs display polyhedra automatically after the user has defined (i) a central atom, (ii) the coordinated atoms and (iii) minimum (often a default of near zero) and maximum bond distances. One exception is Balls&Sticks, where graphical point and click of the mouse is used to define the polyhedra.

3.3.4.2.5. Cartesian coordinates

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Importing Cartesian coordinates can allow the display of incommensurate and quasicrystal structures if the refinement software has this as an output option. Using Cartesian coordinates can sometimes be more convenient for the slight modification of structures for the display of distortions or individual molecules. A structure defined as triclinic with space group P1 and a cubic cell with edges of unit length would also work for importing a structure or molecule originally defined in a Cartesian frame of reference.

3.3.4.2.6. Comparing or overlaying crystal structures

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The graphical comparison of crystallographic structures can be useful and time-saving for comparison of polymorphs or a chemically similar series of small-molecule structures. One program that can perform this function is CrystMol, where multiple molecular structures can be compared using a point and click menu or via the CrystMol scripting system. RMS differences are also listed. Superposition of structures is discussed in Section 3.3.1.2.2[link].

3.3.4.2.7. Extended structures and topology analysis

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Currently, the only available program that rigorously analyses extended structures (involving overlapping or interpenetrating molecules) is OLEX. For graphical viewing of extended structures OLEX displays particular fragments in a single colour. GRETEP also has this display functionality, making it useful for viewing extended structures.

3.3.4.2.8. Magnetic crystal structure display

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The software listed in Tables 3.3.4.1[link] and 3.3.4.2[link] includes programs that can display graphics representing magnetic vectors without necessarily having the ability to understand magnetic symmetry. Programs that can display magnetic structures include ATOMS, CrystalMaker, Diamond, DrawXTL, FpStudio, VENUS and Xtal-3D.

3.3.4.2.9. Incommensurate crystal structures

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PRJMS and FpStudio are currently the only programs that can plot modulated structures in three-dimensional space; FpStudio is currently restricted to incommensurate magnetic structures. However, importing Cartesian coordinates can be used to display incommensurate structures when incommensurate refinement software can output coordinates in this format. BALSAC provides a good example of software which by default uses Cartesian coordinates, from which plots of incommensurate and quasicrystal structures can be generated.

References

International Tables for Crystallography (2005). Vol. G. Definition and Exchange of Crystallographic Data, edited by S. R. Hall & B. McMahon. Heidelberg: Springer.
Cockcroft, J. K. & Stephenson, R. (2005). EPSRC-funded Collaborative Computational Project Number 14 for Single Crystal and Powder Diffraction (CCP14), http://www.ccp14.ac.uk/.
Dowty, E. (2005). Cryscon. Shape Software, 521 Hidden Valley Road, Kingsport, TN 37663, USA. http://www.shapesoftware.com/.
Hummel, W., Raselli, A. & Bürgi, H.-B. (1990). Analysis of atomic displacement parameters and molecular motion in crystals. Acta Cryst. B46, 683–692.








































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