July 1997 - chemweb - imperial.ac.uk

Molecule Editor in Java
by Denis M. Bayada 18 Feb '99

18 Feb '99

Dear all, I have just finished writing a molecule editor in JAVA. If anyone is interested, it is available at : http://www.chem.leeds.ac.uk/ICAMS/people/denis/moledit.html You may freely download the Java source code and modify it. Any comments are indeed welcome. Thank you Denis --------------------------------------------------------------------- Denis M. Bayada e-mail: denis(a)mi.leeds.ac.uk ICAMS voice: (44) (0)113 233 65 95 School of Chemistry fax: (44) (0)113 233 65 63 University of Leeds http://www.chem.leeds.ac.uk/ICAMS/people/denis Leeds LS2 9JT ENGLAND ... but as I proceeded in my labour, it became every day more horrible and irksome to me. Sometimes I could not prevail on myself to enter my laboratory for several days, and at other times I toiled day and night in order to complete my work. It was, indeed, a filthy process in which I was engaged. Frankenstein (Mary Shelley) --------------------------------------------------------------------- ----- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.ch.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to listserver(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Use of "palmtop" computers in chemistry
by Rzepa, Henry 30 Jul '97

30 Jul '97

It appears that the "PDA" generation is finally maturing into a "palmtop" market, with various devices on the market from Apple, US Robotics, HP, and running various types of software. Some of these devices support networking, some only uploads to a "proper" computer, and some can have modems. Does anyone have an example of the application of such devices to chemistry courses, libraries, lab, etc, If so, does it seem whether such devices might have a worthwhile role to play in chemistry, and will provision for their networking need to be thought of? Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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ANNOUNCE: Conference on Visualisation for the Biosciences
by Alan Robinson 28 Jul '97

28 Jul '97

Frontiers in Visualisation and Human-Computer Interaction '97 ------------------------------------------------------------- at The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Cambridge, UK. 10th and 11th December, 1997. http://www.ebi.ac.uk/fiv97/ Introduction: This two day conference will provide an outstanding opportunity to hear some of the world's leading speakers in the related areas of human- computer interaction and visualisation. It will also provide an arena for professionals in the biosciences and pharmacology to meet with the leading graphics and interaction experts and to develop new ideas and synergies. The meeting will take place in the newly completed conference facilities at the Wellcome Trust Genome Campus in the grounds of Hinxton Hall, Cambridge, UK. The campus is the site of The European Bioinformatics Institute, The Sanger Centre and the UK MRC Human Genome Mapping Project Resource Centre. The two keynote speakers are: Professor Andries van Dam, Thomas J. Watson, Jr., University Professor of Technology and Education and Professor of Computer Science, Brown University, Providence, RI (http://www.cs.brown.edu/people/avd/home.html) and Prof. Dr. José Luis Encarnação, Professor Technical University of Darmstadt and Director of the Fraunhofer Institute for Computer Graphics in Darmstadt (http://www.crcg.edu/Staff/enc.html) Both have been visionary pioneers in establishing the discipline of computer graphics, Van Dam being a co-founder of SIGGRAPH and Encarnação being the driving force behind the founding of EUROGRAPHICS. The conference program will cover: Frontiers in 3D Human Interactions Applications of Virtual Reality Distributed Computer-Supported Collaborative Working, CSCW-VR Visualisation in the Biosciences There will also be an opportunity for poster submissions and a trade show. Registration Fee: Before November 10th, the registration fee for the conference is 150 GBP -- Standard Rate 100 GBP -- EBI Industry Affiliates 75 GBP -- EBI BioStandards Partners 75 GBP -- Full-time employees of government, universities, and university-affiliated hospitals The cost of lunches is included in the registration fee. The conference banquet is an additional 35 GBP and will be in The Great Hall of King's College in Cambridge. The closing date for early registration and submission of abstracts is 10th November, 1997. Further information on speakers, hotel accommodation and registration may be found at: http://www.ebi.ac.uk/fiv97/ Yours sincerely, Alan J. Robinson. -- ============================================================ Alan J. Robinson Tel:+44-(0)1223 494625 EMBL Outstation Fax:+44-(0)1223 494468 European Bioinformatics Institute Email: alan(a)ebi.ac.uk Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1RQ, UK http://industry.ebi.ac.uk/~alan/ ============================================================ chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Conference-Biotechnology-Trieste-13-15 October.
by pschwander＠epo.e-mail.com 25 Jul '97

25 Jul '97

As part of the Regional Industrial Property Programme (RIPP) financed by the European Commission under its PHARE programme of assistance for the countries of central and eastern Europe, the European Patent Office is organising a three-day international conference on "Protecting Pharmaceutical and Biotechnological Inventions" on 13 to 15 October 1997 in Trieste, Italy. The aim of the conference is to introduce the latest intellectual property developments in the pharmaceutical and biotechnological sectors at European level. Several themes will be developed such as the counterfeiting of pharmaceutical products, regulations and patents relating to biotechnological products and processes, the mass media and public opinion on the patentability of biotechnology. Speakers at the conference will be representatives and experts from the European Commission, the European Patent Office, the OECD, private companies and other organisations. Representatives of the IP offices of central European countries will present their views on the patenting of pharmaceutical and biotechnological products. The conference is essentially aimed at patent attorneys, decision- makers, scientists and representatives of the industrial sectors concerned. For further information and registration, please contact the European Patent Office (International technical co- operation - RIPP programme): tel.: +49-89-2399.5213; Fax: +49-89-2399.5239; e-mail: dewez(a)epo.e-mail.com. The programme and registration form are also downloadable from Internet at the following URL address: http://www.Austria.EU.net/epo/intcop/trieste.htm. Salutations, Best regards, Paul SCHWANDER c/o Ministere des Affaires economiques / OPRI / Blv. E. Jacqmain 154 / B-1000 Bruxelles chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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The UK Dearing Report into Higher Education
by Paul May 24 Jul '97

24 Jul '97

Hi, > The full (1700 page) Dearing report is on > http://www.ncl.ac.uk/ncihe/index.htm > Anyone finding interesting snippets for chemists, and IT > in particular, do please feel free to post to this list if relevant. Well, these are not specifically about chemistry, but they do relate to Communications, networks, the web and IT in general. It's quite long, but it's still only my small, selected highlights from the whole. ------------extracts from Dearing Report--------- 68. The use of new technologies for learning and teaching is still at a developmental stage but we expect that students will soon need their own portable computers as a means of access to information and for learning via a network. We are also aware that students will need access to high quality networked desktop computers that permit the use of the latest multi-media teaching materials and other applications. Recommendation 46 We recommend that by 2000/01 higher education institutions should ensure that all students have open access to a Networked Desktop Computer, and expect that by 2000/06 all students will be required to have access to their own portable computer. 13.3 We believe that, for the majority of students, over the next ten years the delivery of some course materials and much of the organisation a nd communication of course arrangements will be conducted by computer. Just as most people will come to expect to be connected to, and to make use of, world communications networks in their daily lives, all students will expect continuous access to the network of the institution(s) at which they are studying, as a crucial link into the learning environment. 13.6 Researchers are already beginning to have access to major pieces of equipment and large data banks on a world-wide basis, and this is a facility they will increasingly require and expect. As the knowledge base increases in volume and sophistication, the requirement for such connections will increase. However, the need to duplicate scarce or expensive equipment and resources, including datasets, should be reduced by prudent exploitation of Communications and Information Technology (C&IT). Electronic journals serving a world-wide network of researchers will be common. 13.10 While the effective adoption of C&IT in higher education requires appropriate technology, adequate resources and staff development, success depends on the effective management of change. The development and implementation of an integrated C&IT strategy will be one of the main challenges facing managers of higher education institutions. ...A detailed audit has not been possible, but we estimate that the UK higher education sector currently spends between #800 million and #1 billion a year in total on C&IT ie up to ten per cent of total higher education turnover.....Many institutions could realise significant savings by adopting, and adhering to, a minimum sub-set of open standards for hardware and software. Adopting such standards will lead to the need for less C&IT support, less training and improved mobility of clerical, administrative and technical support staff. 13.16 A standard approach to the acquisition and delivery of electronic information (for example through an Intranet is also needed. Examples would include: techniques to improve the management of the teaching and assessment process; avoiding the duplication of administrative data; computerising student admissions; and drawing together foundation and remedial teaching materials. Other opportunities for savings exist through, for example, the institution-wide use of a single smart card. Recommendation 41 We recommend that all higher education institutions in the UK should have in place overarching communications and information strategies by 1999/2000. 13.21 On our visit to the USA we were particularly impressed by the communications infrastructure developed and adopted by the Harvard Business School. This Intranet-based system of teaching and administration was established across the entire School due to determined management, including at the highest level, and a dedicated and skilled implementation team. Recommendation 42 We recommend that all higher education institutions should develop managers who combine a deep understanding of Communications and Information Technology with senior management experience. ...JANET traffic has risen 25-fold, from approximately 40 Gigabytes (40,000,000,000 bytes) a day three years ago, to around 1 Terabyte (1,000,000,000,000 bytes) a day in 1997... We recognise that networks, previously most heavily used by the research community, are now also being more regularly used to support learning and teaching and other activities and that this might eventually reduce access to networks needed by researchers. We believe that increased investment in the network capacity will be essential if researchers are to continue to make good use of centrally provided high performance computing. 13.27 JANET is extensively used. A recent survey of academic staff connected to JANET found that 98 per cent used electronic mail at least once a week and 92 per cent reported that they found it *essential* or *very useful*. Use of and benefit from other technologies, such as video-conferencing, was found to be less widespread and was identified by only a minority of respondents, but the study noted that this 'probably reflects the availability of the technology rather than... the number of users who would use the faciliAOes if they were more widely available'. Although new (Metropolitan Area Networks) MANs are being planned and built, there are still significant areas of the UK which are not covered. We, therefore, commend the further development of MANs where the Funding Bodies and institutions consider that these are technically and financially sensible. 13.31 Multi-media electronic information available over the network can provide valuable and important building blocks for course material. We see this as a development of growing importance and value. Close liaison is therefore needed between providers of such material and the proposed Institute for Learning and Teaching in Higher Education and, in particular, with any company created to produce, commission and market on-line learning and teaching materials. 13.36 As a significant proportion of higher education is delivered in further education colleges, we consider that all further education institutions should have access to the higher education network, either directly or via a secondary connection to a local higher education institution. Recommendation 44 We recommend to the Government and the Funding Bodies that, to harness and maximise the benefits of Communications and Information Technology, they should secure appropriate network connectivity to all sites of higher education delivery and further education colleges by 1999/2000, and to other relevant bodies over the medium term. 13.38 The predicted demand and growth in network traffic and requirement for enhanced bandwidth will result in significant additional costs, year-on-year, to the sector, and the Joint Information Systems Committee (JISC) has signalled the introduction of tariffs in the future. We are not opposed in principle to the introduction of tariffs, provided that such tariffs offer value for money to customers and do not unreasonably limit access to quality materials and services to those customers least able to pay. Cost should not be an obstacle to pervasive broadband access, nor should it inhibit growth in the use and availability of quality learning materials and information resources. Our immediate concern is that the swift and sudden introduction of tariffs would have a dampening and damaging effect on development and use of such materials. We therefore consider that the introduction of tariffs should be withheld until 2000/2001 and that thereafter tariffs should be phased in. 13.39 As students gradually require increased access to networks, it will become more important for institutions to supply networking to student residences (as many are already doing) and to offer dial-up connectivity to students in their own homes. Recommendation 45 We recommend that institutions of higher education, collectively or individually as appropriate, should negotiate reduced tariffs from telecommunications providers on behalf of students as soon as possible. 13.43 Over the next ten years, all higher education institutions will, and should, progressively move significant aspects of administration and learning and teaching to the computer medium. They should be planning for this now. The development of powerful paperback-sized notebook computers, capable of sending and receiving e-mail and accessing the Internet, is envisaged within the next few years. We expect that this technology will be harnessed by students and institutions for learning and teaching and administration through the development of a Student Portable Computer (SPC). 13.44 The SPC will store basic course information and enable the student to undertake a significant amount of work off-line (for example drafting of assignments). It will also allow the student, via a network connection, to access electronic information (such as timetables, course materials and library catalogues), to submit assignments, and to communicate with tutors and other students. It is possible that the SPC might be a fully mobile device accessing the network through wireless technology. We found, on our visit to the USA in January 1997, that an SPC (usually an industry-standard laptop computer) is already a requirement for courses at a number of institutions. The same requirement applies to some UK programmes. 13.45 To use their SPCs effectively in this way, to communicate and send and receive information, students will require daily access to the network. There will, therefore, need to be adequate provision of network connection ports in institutions into which students can plug their SPCs and there should be provision of dial-up connectivity for off-campus students at each institution. 13.46 At least in the short term, the widespread availability of SPCs will not obviate the need for Networked Desktop Computers within the campus. 13.47 As access to a Student Portable Computer (SPC) becomes a standard requirement for a student, we envisage that it will represent part of a growing market for such hardware, comparable with the mobile phone market which has burgeoned in recent years. Thus the SPC will be a relatively standard product in an open and competitive market. 13.49 We suggest that the SPC is funded by students themselves with some assistance for the transitional phasing of its introduction from the National Lottery. We note that the proposed Millennium Information and Communication Technology Fund may come into being in 2000 to distribute around #300 million per annum. In the interests of keeping prices as low as possible for the student purchaser we also propose that institutions assume a role in the distribution of the SPC and that the Government should give consideration to allowing tax credits for hardware suppliers of this product. Networked Desktop Computer 13.50 Networked Desktop Computers (NDCs) need to be of a sufficiently high technical specification to make full use of the network and networked services, and permit the use of the latest interactive multimedia learning and teaching materials and other applications (whether accessed via the network or CD-ROM). They must, therefore, incorporate up-to-date sound, video and graphics technology. 13.51 Existing evidence suggests that, at present, the ratio of students to desktop computers in higher education institutions is only slightly better than 15:1 across the UK. In the short term, student access to NDCs needs to be improved across the sector as a whole. The required ratio will vary from institution to institution, depending on such factors as subjects taught, types of student and learning and teaching methods. A ratio of 10:1 would be a good standard at present but this needs to improve to 8:1, particularly where an institution makes extensive use of on-line learning materials and electronic information services. We expect that, as such methods become widespread, a ratio of 5:1, or better, will be necessary for multi-faculty institutions. Recommendation 46 We recommend that by 2000/01 higher education institutions should ensure that all students have open access to a Networked Desktop Computer, and expect that by 2005/06 all students will be required to have access to their own portable computer. 13.55 Value-added tax (VAT) is payable, at the full rate, on electronically published materials, but no VAT is currently charged on printed materials. The current arrangements inhibit the development and use of electronic materials as an alternative to print-based materials. To minimise this adverse effect the rate of VAT levied on electronic materials should be reduced and maintained at the lowest level possible. Conclusion 13.57 We have been impressed by the high standard of Communications and Information Technology (C&IT) provision in UK higher education and the enthusiasm of the many dedicated experts who are pioneering its extended use. We believe that the successful exploitation of C&IT is pivotal to the success and health of higher education in the future, as it has been since the first computers were built at Manchester and Cambridge. We do not consider that the barriers to this are financial, indeed the sector already spends a significant amount in pursuit of such activities. We consider that this expenditure warrants closer attention at the institutional level. What will be required, however, is a fundamental rethink of institutional priorities, an equally essential change of culture, and well-informed leadership. Above all, there remains an urgent need for institutions to understand better and respond to the challenges and opportunities of the emerging information age. ====================== Regards, ------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 9287667, fax: +44 (0)117 9251295 <mailto:paul.may@bris.ac.uk> <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> "The Psi-Corps is your friend. Trust the Corps." Babylon 5 ------------------------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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X-ray Software
by David Bradley Science Writer 24 Jul '97

24 Jul '97

Slightly off the beaten track for this list. Does anyone have a pointer to a round-up of current X-ray crystallography software? TIA Dave Bradley ------------------------------------------------------- | David Bradley Science Writer | | Bradley(a)enterprise.net | | Tel/Fax +44 1223 440834 | | | | Elemental Discoveries: chemical happenings on the web | | http://homepages.enterprise.net/bradley/elem1.html | | | ------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Re: X-ray Software
by Jonathan W. Steed 24 Jul '97

24 Jul '97

In Response to David Bradley's request, here are some helpful web sites: Intl. Union of Crystallography: http://www.iucr.ac.uk/welcome.html British Crystallographic Assocn.: http://www.cryst.bbk.ac.uk/BCA/index.html Crystallography World Wide: http://www.unige.ch/crystal/w3vlc/crystal.index.html (a pointer to almost all Xtallog resources, including software UCL Crystallography Page: http://www.ucl.ac.uk/chem/resources/crystal/index.htm Cambridge Xtallog database: http://www.ccdc.cam.ac.uk/ SHELX Home page: http://linux.uni-ac.gwdg.de/SHELX/ Crystallog World wide, Cambridge database, SHELX and UCL Homepage especially all have software pointers. There is some more data on instrument manufacturers etc etc in my home page, URL below. Hope this is of some use. Jon. Dr. Jonathan W. Steed Department of Chemistry, King's College London, Strand, London WC2R 2LS, UK. Tel: +44 (0)171 873 2117, Fax: +44 (0)171 873 2810 e-mail: jon.steed(a)kcl.ac.uk Web site: HTTP://CRAC3.CH.KCL.AC.UK/KCLCHEM/SUPRAMOL.HTM chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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RE: X-ray Software
by Stansfield, Rob, HMR/US 24 Jul '97

24 Jul '97

David, Try <http://www.iucr.ac.uk/sincris-top/index.html> and follow the "Software database" link to <http://www.iucr.ac.uk/sincris-top/logiciel/>. Regards, Rob ________________________________________________________ Rob Stansfield, Selectide Corporation / Hoechst Marion Roussel, Inc. 1580 East Hanley Boulevard, Tucson, AZ 85737-9525, USA Tel: +1-520-544-5805 Fax: +1-520-575-8283 Internet: robstansfield(a)hmri.com www: http://www.primenet.com/~rob3d/rob.html ________________________________________________________ ---------- From: David Bradley Science Writer[SMTP:Bradley@enterprise.net] Sent: Wednesday, July 23, 1997 12:55 PM To: chemweb(a)ic.ac.uk Subject: X-ray Software Slightly off the beaten track for this list. Does anyone have a pointer to a round-up of current X-ray crystallography software? TIA Dave Bradley ------------------------------------------------------- | David Bradley Science Writer | | Bradley(a)enterprise.net | | Tel/Fax +44 1223 440834 | | | | Elemental Discoveries: chemical happenings on the web | | http://homepages.enterprise.net/bradley/elem1.html | | | ------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk) chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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The UK Dearing Report into Higher Education: Implications for chemistry
by Rzepa, Henry 23 Jul '97

23 Jul '97

The full (1700 page) Dearing report is on http://www.ncl.ac.uk/ncihe/index.htm It contains 95 recommendations, quite a few of which relate to IT matters. No doubt over the next few weeks the implications will start to filter through. Anyone finding interesting snippets for chemists, and IT in particular, do please feel free to post to this list if relevant. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; mailto:rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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Showing H-bonding using CHIME
by M Cole 22 Jul '97

22 Jul '97

Hi there, I am trying to generate an inorganic crystal structure (using CHIME via an XYZ file format) where the structure involves a fair degree of H-bonding which I want to illustrate (by toggling on and off). However when I choose the H-bonding option (using the mouse control), the H-bonding is not indicated. Does anyone have any idea what I might be doing wrong ? For example do I have to specify in the dataset the pairs of atoms that are involved in H-bonding ? My typical O-H H-bond distance is 1.7-1.8 Angstroms. Are there limits which H-bonding is only shown when using CHIME ? Thanks Mike Cole Chemistry Department Manchester Metropolitan University UK chemweb: A list for Chemical Applications of the Internet. Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To unsubscribe, send to majordomo(a)ic.ac.uk the following message; unsubscribe chemweb List coordinator, Henry Rzepa (rzepa(a)ic.ac.uk)

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