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X-Ray Crystallography - Software

 

Crystallography and Chemistry Databases

 

1. CSD - Cambridge Structural Database

The "organic" crystallographic data base. Features everthing with at least one C-H fragment. The CSD is provided by the Cambridge Structural Data Centre. Purdue students, staff and faculty can access WebCSD at http://webcsd.ccdc.cam.ac.uk.ezproxy.lib.purdue.edu/, or they can install the full unlimited version of the CSD, available for all common operating systems. The data base includes a copy of Mercury with all features fully enabled. Please contact the crystallographer for access to the full licensed version of the CSD and Mercury and for installation and setup instructions.

 

2. ICSD - Inorganic Structural Database

The ICSD contains information on inorganic crystal structures including pure elements, minerals, ceramics, inorganic salts, metals, and intermetallic compounds, including their atomic coordinates. It is updated semiannually, each time adding approximately 3000 new records. As of 2018, the database contains ca. 193,000 entries. The database is available for Purdue users at https://icsd.fiz-karlsruhe.de/search/basic.xhtml (campus computers only).

 

3. ICDD - Powder Diffraction File PDF

The PDF is published by the International Centre for Diffraction Data ICDD (http://www.icdd.com/). It is the most extensive and comprehensive collection of powder and single crystal diffraction data with hundreds of thousands of entries from all fields of structural science with databases available for organics and organometallics, pharmaceuticals, exipients, polymers, metals and alloys, ceramics, minerals and related materials. It is updated annually. A copy is available for Purdue users on the control computer of the Panalytical Empyrean X-ray diffractometer in Wetherill 101. Please contact Dr. Zeller (zeller4@purdue.edu) for access to the instrument and computer (no instrument training is required to access the data base).

 

4. Scifinder

"The" chemistry database, formerly Chemical Abstracts Service. Available for Purdue students, faculty and staff via the Chemistry Library's web page. Purdue login required.

 

5. International Tables of Crystallography

The International Tables of Crystallography are the definitive resource and reference for all work in crystallography. The series comprises articles and tables of data relevant to crystallographic research and to applications of crystallographic methods in all sciences concerned with the structure and properties of materials. Emphasis is given to symmetry, diffraction methods and techniques of crystal structure determination, and the physical and chemical properties of crystals. Each volume also contains discussions of theory, practical explanations and examples. The tables can be accessed via http://it.iucr.org.ezproxy.lib.purdue.edu/ (campus computers only).

 

Graphics Software

 

1.  Mercury

Mercury is provided by the Cambridge Structural Data Centre and is available for all types of operating systems. A free version is available from their web page, at http://www.ccdc.cam.ac.uk/Solutions/CSDSystem/Pages/Mercury.aspx. Purdue students and faculty can install the full unlimited version of Mercury, available with the Cambridge Structural Database, CSD. Mercury is the most user friendly of the standard XRD graphics programs, but some adjustments to the default settings are recommended if you want to create high quality high resolution images. Step-by-step instructions for setting up CCDC's Mercury to create high quality Ortep-like figures for publications and presentations can be found here. One major drawback of Mercury is its inability to handle disorder well, and labelling atoms is cumbersome. Please contact the crystallographer for access to the fully licensed version of Mercury and for installation and setup instructions.

 

2.  Vesta

VESTA is a 3D visualization program for displaying structural models for both molecular ("organic") and solid state ("inorganic") materials. It can be used to create polyhedral as well as molecular plots, but its capabilities are going way beyond simple displaying of crystal structures. It can be used to create polygons on isosurfaces, display volumetric data such as electron/nuclear densities, magnetic properties, and crystal morphologies. It supports lattice transformation from conventional to non-conventional lattices including superlattices and sublattices. For a full list of VESTA's capabilities please visit the VESTA page at http://jp-minerals.org/vesta/en/. VESTA runs on Windows, Mac OS X, and Linux. It is contributed free of charge for non-commercial users.

 

3.  PLATON for Windows  (available from http://www.chem.gla.ac.uk/~louis/software/platon)  

This large program package is a complete crystallography toolbox. It provides a large part of the IUCR's checkcif procedures, and has highly sophisticated features to check for missed symmetry and for handling of diffuse or highly disordered solvents. While most users will not make use of many of the features it does have interactive ORTEP and other graphics capabilities. This package consists of two zipped files, "pwt" and "platon". To install, unzip both and then move the file platon.exe to the same directory as pwt.exe.  Running pwt.exe will start Platon.  

Instructions for using Platon can be found at http://www.cryst.chem.uu.nl/platon.

 

4.  ORTEP-3 for Windows (available from http://www.chem.gla.ac.uk/~louis/software/ortep/index.html)

This is an interactive version of the standard ORTEP program and is menu driven. This package requires a license which can be obtained from the web site.

 

5.  The IUCr publcif tools page, at http://publcif.iucr.org/services/tools/, the by far easiest way to make publication quality tables and figures. Its interactive figure utility utilizes ORTEP in the background. No license is required.

 

 

Structure Refinement Software

 

1.  SHELXL-2018

THE crystal structure refinement program. It replaces the now deprecated XL-97 and earlier versions of Shelxl. A copy of Shelxl2018 can be obtained from the author, George Sheldrick, at http://shelx.uni-goettingen.de/. Registration is required.

 
2.  The Shelxtl Package 

This program is proprietary software of Bruker AXS and requires a license. It may be used by students and faculty who are registered users of the Purdue X-ray facility. The program XPREP, part of the package, is commonly used to check a dataset for symmetry, assign a space group and set up files for use with solution programs such as XS, XM or XT. The files created by the package (*.ins and *.res files) are the starting models in a crystal structure refinement process using Shelxl-2018.


3.  SHELXLE

A graphical interface for use with Shelxl2018 that is fully compatible with all commands and procedures of Shelxl-2018. In the view of the Purdue crystallographer the by far best and most versatile graphical interface for Shelxl, featuring difference electron density maps, interactive symmetry tools, automatic backups, and many other features that make advanced crystal structure refinement easy and efficient. It is available from the author at https://www.shelxle.org. Registratration is encouraged, but not required. Shelxle is available for all major operating systems. It it is subject to continuous improvements and should be updated on a regular basis.

 

4. OLEX

An alternative graphical interface predating SHELXLE, with similar features. It is available at http://www.olexsys.org/, registration is required. OlexSys Crystallography applications and modules are available for all major operating systems. It has a large number of "added features" that can substantially streamline the refinement of a crystal structure, especially in the hands of a novice user. It does however not follow the coding of Shelxl as strictly as Shelxle which can be problematic when trying to explain what happens "under the hood" for a complicated structure refinement, and it is not 100% compliant with PLATON and Checkcif requirements.

 

5. CRYSTALS

An alternative to Shelxl-2018, with its own graphical interface. It is available at http://www.xtl.ox.ac.uk/crystals.1.html. Having its own least squares and refinement algorithm makes it distinct from Shelxl-2018, with advantages and drawbacks. The most serious drawback is that most checking programs are written for Shelxl, and files created by CRYSTALS are sometimes not compatible with IUCr checkcif procedures.

 

Miscellaneous Software

1.  Encifer (available from http://www.ccdc.cam.ac.uk/free_services/encifer)

All crystallographic data are submitted to journals using the Crystallographic Information Format, CIF.  This file must be edited to include instrument and software details, and for some journals also authors and other information. The editor Encifer is the easiest way to do this.

 

2.  Publcif (available from http://journals.iucr.org/services/cif/publcif/)

publCIF takes a crystallographic information file (CIF) and prepares a formatted paper (Preprint) in the style of Acta Crystallographica Sections C and E, and IUCrData. The CIF and the Preprint are presented side-by-side and are both editable. Changes made to one are applied to the other as you type. publCIF employs extensive CIF syntax and dictionary compliance checking, both as you type and when specifically requested. In addition, it provides a number of editorial tools to help you write your paper in the style required by IUCr journals.

 

 

Installing XRD Software on your own computer (Single Crystal XRD)

 

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