 | Acta Crystallographica Section A Acta Crystallographica Section A FOUNDATIONS AND ADVANCES |
journal menu
feature articles
| FOUNDATIONS ADVANCES |
Nexus, crystallographic computing all around the world
aNational Research Council of Canada, Chalk River Laboratories, Chalk River, Ontario K0J 1P0, Canada, and bDepartment of Chemistry, University College London, Christopher Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, UK
*Correspondence e-mail: lachlan.cranswick@nrc.gc.ca
Crystallographic Nexus CD-ROMs, containing a range of free crystallographic software for single-crystal and powder diffraction available on the Internet, have been distributed on request since 1996. The free CD is made in the form of a `virtual Internet' with the main intent of benefiting crystallographers with inadequate Internet access. The IUCr funds an annual/biennial update which is distributed to known previous recipients. Feedback from current recipients indicates the CD is still useful. The most current IUCr-funded CD is being produced by the CCP14 project at University College London and The Royal Institution UK for distribution to the ECM 2007 and AsCA 2007 conferences.
Keywords: CD-ROM; crystallographic software; Internet; powder diffraction; single crystal.
1. Introduction
For more than a decade, the Internet has allowed access to a range of free, modern, crystallographic analysis software. This software can help build an effective software toolkit for crystallographic research and teaching. In the mid 1990's, Internet use in the far reaches of the globe was described as `booming' (Butler, 1996![[Butler, D. (1996). Nature (London), 380, 377-381.]](../../../../../../logos/arrows/a_arr.gif "Butler, D. (1996). Nature (London), 380, 377-381.")
). However, information from crystallographers indicated otherwise, that Internet access for academics and students in less technically advanced regions was generally unavailable, inadequate, costly; and, if available at all, often restricted to e-mail. As computational analysis is crucial in crystallography, there was, and still is, a challenge to ensure access to a range of crystallographic analysis tools.
2. Nexus CD creation and distribution
To help mitigate poor Internet access for affected crystallographers and students, a free CD-ROM was initiated in mid-1996 that contained a variety of crystallographic software and Internet resources. The free CD-ROM was regularly updated and air-mailed on request irrespective of the person's geographic location. The aim of the CD was to put relevant parts of the crystallographic Internet into a form suitable for scientists and students with poor Internet access. The CD provides recipients with modern free crystallographic tools and information for structure analysis and teaching.
Around the mid 1990's in Australia, home- and small-office-based CD writing hardware was becoming generally affordable, enabling the creation of CD-ROMs without professional assistance. For initial versions of the Nexus CD, it was a challenge using a 28000 baud modem-based link to the Internet to fill up the then massive CD-ROM space of 650 MB with useful crystallographic material. As years progressed, with broadband Internet, more powerful computer hardware and software distributions of much larger size, the problem changed to one of 650 MB becoming an increasingly small space in which to fit a range of crystallographic software and resources.
Current grabbing of programs and web content is performed with the program Grab-a-Site for MS-Windows 95 (Blue Squirrel, 1998), using a residential 768 kB DSL connection and personal laptop PC computer with Intel CPU running Microsoft Windows XP. Downloading content for the CD-ROM, CD creation and burning is reliable and routine. The time and cost to create CDs has reduced considerably since the mid-1990's (Tables 1–3).
| ||||||||||||||||||||||
| ||||||||||||||
| ||||||||||||||||||||||||||||||
3. Software included on the CD-ROM
The content on the CD-ROM varies to fit within CD-ROM size constraints, with emphasis on including multiple packages that perform similar crystallographic analyses. In the 2006 version of the CD, small-molecule single-crystal suites included Crystals, WinGX and PLATON. Single-crystal structure solvers included Crunch, DIRDIF, SuperFlip and programs available within Crystals, WinGX and PLATON. Freestanding powder indexing programs on the CD were Treor, Ito, Dicvol2006 and McMaille. Powder indexing suites were Crysfire, Fullprof-Winplotr and Chekcell, with powder structure-solution programs Fox and ESPOIR. A variety of Rietveld, structure drawing and utility programs were included, as well as a portion of the IUCr website including Crystallography Online. The source code within Armel Le Bail's Crystallography Source Code Museum is also included (Le Bail, 2002). A list of software on the CD-ROM is provided in Table 4.
|
4. Distribution of the CD-ROM
Numbers of CD-ROMs sent sorted by country are given in Table 5. Some institutes and departments reported further duplication of the CD, followed by redistribution to colleagues in their institute and region.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The current procedure for generating and mailing a Nexus CD is similar to that in 1996. On receiving a request for a CD-ROM, a current version of the CD is burnt and sent via air-mail. Availability of the CD was advertised in the relevant Internet newsgroups, IUCr newsletters, conferences and by word of mouth from prior recipients. The rate at which CDs were sent to new recipients over the last ten years varied from zero to around twenty per month. Current rates at which new requests for CDs are received average around one per month.
5. Yearly distribution of an updated CD-ROM
Since 2000, the IUCr (via the Committee for Electronic Publishing, Dissemination and Storage of Information) has funded regular annual or biennial updates of the CD-ROM, distributed via air-mail to all previous recipients. The intent has been to achieve one version per year, preferably timed to coincide with a suitable crystallographic conference to achieve extra distribution. The most recent IUCr-funded distribution was in June 2007, being produced by the CCP14 project at University College London and The Royal Institution, London, UK. This timing was for distribution to the ECM 2007 conference in Morocco and AsCA 2007 conference in Taiwan, as well as the usual air-mailing distribution to previous recipients.
6. Internet accessibility and CD-ROM usage
As there has been no requirement for recipients to report usage of the CD-ROM, a questionnaire was sent in January 2007 to the e-mail addresses of CD-ROM recipients. The questions and responses are given in Table 6. Questions were multiple choice to minimize time needed to answer, with options for more elaboration if required. To encourage accurate negative responses, a preamble to the questionnaire emphasized that replies should admit to no longer requiring the CD-ROM if that was currently the case.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Of the 402 unique e-mail addresses to which the questionnaire was sent, e-mails to 121 of the addresses bounced and 43 responses were received. The number of bounced e-mails is not necessarily that surprising as one of the authors (LMDC) is on his sixth new e-mail address since 1996, previous e-mail addresses being defunct due to changes of employer, Internet Service Providers or an account being overwhelmed with junk e-mail.
Of the 43 responses, powder diffraction usage was almost double that of single-crystal diffraction. The majority of respondents indicated that downloading of crystallographic software via the Internet ranged from `problematic but do-able' to `not practical'. Of the 14 respondents that indicated downloading of crystallographic software via the Internet was `routine and easy', 12 indicated a preference for still receiving the Nexus CDs in future as a convenient back-up of crystallographic software. 13 respondents were from India and six from China. Within India and China, responses varied from the Internet accessibility being `routine and easy' to `not practical'. This could indicate that difficulties with academic and student access to the Internet may involve regional issues and types of scientific facility.
Acknowledgements
The following are thanked for suggestions, permissions and assistance in producing the Nexus CD-ROMs. Web content owners and custodians for permission to include material on the Nexus CD-ROM: Dr Armel Le Bail of the University of Le Mans, France; Dr Alan Hewat of ILL, Grenoble, France; Dr Howard Flack of the University of Geneva, Switzerland; and Mr Tony Sanderson of CSIRO Division of Minerals, Australia (deceased) for suggestions and encouragement of the initial versions of the CD-ROM. Dr Stephen Fletcher of CSIRO Division of Mineral Products, Melbourne, Australia (currently Professor of Inorganic Chemistry at the University of Loughborough, UK) for recommending the name `Nexus' for the CDROM. Professor I. David Brown of McMaster University, Ontario, Canada, for assistance in distributing current versions of the CD-ROM, and comments on an initial draft of the text. Dr Richard Stephenson, previously of the CCP14 Project, University College London, UK, for arranging duplication and distribution of the 2005 batch-produced version of the CD.
References
Altermatt, U. D. & Brown, I. D. (1987). Acta Cryst. A43, 125–130. CrossRef CAS Web of Science IUCr Journals Google Scholar
Bergmann, J., Friedel, P. & Kleeberg, K. (1999). IUCr Commission on Powder Diffraction Newsletter, No. 21, p. 5. Google Scholar
Bergmann, J. & Kleeberg, K. (1998). IUCr Commission on Powder Diffraction Newsletter, No. 20, pp. 5–8. Google Scholar
Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487. Web of Science CrossRef IUCr Journals Google Scholar
Beurskens, P. T., Beurskens, G., Bosman, W. P., de Gelder, R., Garcia-Granda, S., Gould, R. O., Israel, R. & Smits, J. M. M. (1996). The DIRDIF96 Program System, Technical Report of the Crystallography Laboratory, University of Nijmegen, The Netherlands. Google Scholar
Blue Squirrel (1998). Grab-a-Site for Windows version 3.0.14, 686 E. 8400 South Sandy, Utah, 84092, USA, http://www.bluesquirrel.com/products/grabasite/. Google Scholar
Boultif, A. & Louër, D. (2004). J. Appl. Cryst. 37, 724–731. Web of Science CrossRef CAS IUCr Journals Google Scholar
Bowden, M. E. (2000). IUCr Commission on Powder Diffraction Newsletter, No. 23, p. 21. Google Scholar
Burnett, M. N. & Johnson, C. K. (1996). Report ORNL-6895, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA. Google Scholar
Butler, D. (1996). Nature (London), 380, 377–381. CrossRef Google Scholar
Cheary, R. W. & Coelho, A. (1992). J. Appl. Cryst. 25, 109–121. CrossRef CAS Web of Science IUCr Journals Google Scholar
Cheary, R. W. & Coelho, A. A. (1998). J. Appl. Cryst. 31, 862–868. Web of Science CrossRef CAS IUCr Journals Google Scholar
Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565. CrossRef IUCr Journals Google Scholar
Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838. CrossRef CAS IUCr Journals Google Scholar
Favre-Nicolin, V. & Černý, R. (2002). J. Appl. Cryst. 35, 734–743. Web of Science CrossRef CAS IUCr Journals Google Scholar
Finger, L. W., Kroeker, M. & Toby, B. H. (2007). J. Appl. Cryst. 40, 188–192. Web of Science CrossRef CAS IUCr Journals Google Scholar
Gelder, R. de, de Graaff, R. A. G. & Schenk, H. (1993). Acta Cryst. A49, 287–293. CrossRef Web of Science IUCr Journals Google Scholar
Gould, R. O., Moulden, N. & Taylor, P. (1988). Department of Chemistry, University of Edinburgh, Scotland. Google Scholar
Holland, T. J. B. & Redfern, S. A. T. (1997). Mineral. Mag. 61, 65–77. CrossRef CAS Web of Science Google Scholar
Izumi, F. (2003). J. Ceram. Soc. Jpn, 111, 617–623. Web of Science CrossRef CAS Google Scholar
Kraus, W. & Nolze, G. (1996). J. Appl. Cryst. 29, 301–303. CrossRef CAS Web of Science IUCr Journals Google Scholar
Krumm, S. (1997). WinFit 1.2.1, Institut fur Geologie, Scholssgarten 5, 91054 Erlangen, Germany. Google Scholar
Larson, A. C. & Von Dreele, R. B. (2004). GSAS. Generalized Structure Analysis System. Manual, LAUR 86-748, Los Alamos National Laboratory, Los Alamos, NM, USA. Google Scholar
Laugier, J. & Bochu, B. (2004). LMGP-Suite. Suite of Programs for the Interpretation of X-ray Experiments, ENSP/Laboratoire des Materériaux et du Génie Physique, BP 46, 38042 Saint Martin d'Hères, France. Google Scholar
Le Bail, A. (2001). Mater. Sci. Forum, 378–381, 65–70. Web of Science CrossRef CAS Google Scholar
Le Bail, A. (2002). Crystallography Source Code Museum, http://www.cristal.org/museum/. Google Scholar
Le Bail, A. (2004). Powder Diffr. 19, 249–254. Web of Science CrossRef CAS Google Scholar
Lutterotti, L., Ceccato, R., Dal Maschio, R. & Pagani, E. (1998). Mater. Sci. Forum, 278–281, 93–98. Web of Science CrossRef Google Scholar
Lutterotti, L., Matthies, S. & Wenk, H.-R. (1999). Proceedings of the Twelfth International Conference on Textures of Materials (ICOTOM-12), Vol. 1, p. 1599. Google Scholar
Madsen, I. C. & Hill, R. J. (1994). J. Appl. Cryst. 27, 385–392. CrossRef CAS Web of Science IUCr Journals Google Scholar
Ozawa, T. C. & Kang, S. J. (2004). J. Appl. Cryst. 37, 679. CrossRef IUCr Journals Google Scholar
Palatinus, L. & Chapuis, G. (2007). J. Appl. Cryst. 40, 786–790. Web of Science CrossRef CAS IUCr Journals Google Scholar
Petricek, V., Dusek, M. & Palatinus, L. (2000). Jana2000. The Crystallographic Computing System, Institute of Physics, Praha, Czech Republic. Google Scholar
Proffen, Th. & Neder, R. B. (1999). J. Appl. Cryst. 32, 838–839. CrossRef CAS IUCr Journals Google Scholar
Rodríguez-Carvajal, J. (2001). IUCr Commission on Powder Diffraction Newsletter, No. 26, pp. 12–19. Google Scholar
Rodríguez-Carvajal, J. & Roisnel, T. (1998). IUCr Commission on Powder Diffraction Newsletter, No. 20, pp. 35–36. Google Scholar
Rohlíček, J. & Hušák, M. (2007). J. Appl. Cryst. 40, 600–601. Web of Science CrossRef IUCr Journals Google Scholar
Rupp, B. (1988). Scr. Metall. 22, 1. Google Scholar
Shirley, R. (2002). The Lattice Press, 41 Guildford Park Avenue, Guildford, Surrey GU2 7NL, England. Google Scholar
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Web of Science CrossRef CAS IUCr Journals Google Scholar
Toby, B. H. (2001). J. Appl. Cryst. 34, 210–213. Web of Science CrossRef CAS IUCr Journals Google Scholar
Toby, B. H. (2005). J. Appl. Cryst. 38, 1040–1041. CrossRef CAS IUCr Journals Google Scholar
Watkin, D. J., Prout, C. K. & Pearce, L. J. (1996). CAMERON, Chemical Crystallography Laboratory, University of Oxford, Oxford, UK. Google Scholar
© International Union of Crystallography. Prior permission is not required to reproduce short quotations, tables and figures from this article, provided the original authors and source are cited. For more information, click here.
| FOUNDATIONS ADVANCES |
