CAOS/CAMM Newsletter, #22, February 1995

Summary in English


Clearing VMS space

Users are requested to check their files on VMS and copy the files they want to keep to the Unix system. See the next issue, #23, for a detailed description of the file transfer menu.
In due time we will remove all file, except those belonging to VMS applications like ORAC and CSD.

J.W. Boiten, Ph.D.

On February 24 our colleague Jan Willem Boiten defended his thesis, titled: Computer Methods in Organic Synthesis Design; new and improved algorithms for data conversion, synthesis planning, and 3D perception.
Data conversion refers to a for the Center practical subject: the creation of ORAC databases from REACCS databases, with minimal loss of information.
The chapter on synthesis planning analyzed the performnace of LHASA handling a notorious problem, the synthesis of the desogestrel molecule. It resulted in the development of a new module for polyene cyclisations, a 'zipper'-type of reaction.
The third subject was 3D perception, to predict stereochemistry and stereoselectivity. Most effort was put into improvement of the LHASA 3D builder.
The model reaction was the hydride reduction of ketones, for which it was shown that a simple model could simulate electronic effects rather well. Good enough for implementation in LHASA.

WWW conference for organic chemists

The first Electronic conference for discussing Trends in Organic Chemistry will be held during 12-23 June 1995 on the Global Internet using electronic mail and the World-Wide Web as delivery mechanisms, and organised under the guidance of an international scientific committee.
This pioneering forum offers a novel, low cost and near-instant mechanism for discussing chemistry, with features such as full colour structure diagrams, "clickable" reaction schemes, rotatable 3D molecular images, key-word searches of conference proceedings, and access to a conference "molecular hyper-glossary". See issue 3, 1995 of Chemical Communications for further details and J. H. Krieger and D. L. Illman, Chem. & Eng. News, 1994 (December 12), 29 for details of the previous ECCC conference organised along similar lines. Contributions will take the form of a number of invited Keynote papers, together with submitted papers, conference posters, and electronic mail discussions, in all areas of contemporary organic chemistry, including synthesis, structure, mechanism, physical organic, new materials, bio-organic and computational studies. Papers and posters will be subjected to the peer review process and we expect will be published on a conference CD-ROM which will be abstracted by Chemical Abstracts.

The deadline for submission of abstracts of papers or posters is April 28, 1995. Conference information and details of how to submit contributions are available by the following mechanisms;

  1. Sending an electronic mail to listserver@ic.ac.uk with the single line message; info ectoc
  2. Connecting to the following World-Wide Web location using a browser such as Mosaic or Netscape; http://www.ch.ic.ac.uk/ectoc/
  3. By anonymous ftp file transfer of the file ectoc.txt in the directory pub on the server ftp.ch.ic.ac.uk

Oxford Molecular Ltd software

The December 1994 release of the ASSIST package by Oxford Molecular Ltd. is installed. It concerns Abm (Immunoglobulin domain modelling software), ASP (automated similarity package based on electrostatics), CAMELEON (sequence analysis) and IDITIS (protein database retrieval software) in particular.
New is VAMP, developed by T. Clark at the Universität Erlangen-Nürnberg.

In computro solvation

Solvation models used by the semiempirical packages:
MOPAC: the Conductor-like Screening Model (COSMO, Andreas Klamt, Perkin Transactions 1993, 799).
VAMP: the Self-Consistent Reaction Field (G. Rauhut en T. Clark, J..Am. Chem.Soc. 1993, 115, 9174).
AMPAC: the solvatation model AMSOL by Cramer and Trular (J.Am.Chem.Soc. 1991, 113, 8305, 8552, 9901).

GDB & OMIM Services back on-line!

The CAOS/CAMM Center GDB and OMIM services are now back and fully operational, as of Feb. 2.
In re-implementing the GDB and OMIM services, we have used new (or newer) equipment and redesigned the storage of the data; this new configuration should provide a service that is faster AND more reliable. And, as before, updated each day to be current with the information held in GDB Baltimore.

World Wide Web Tutorial!

The GDB and OMIM General User course we offer here at the CAOS/CAMM Center is now available via the World Wide Web. If you have a WWW Browsing tool, like NCSA Mosaic, Netscape or MacWeb, connect to URL:
http://www.caos.kun.nl/genomics/GDB_OMIM_TOC.html
and try it out!
The tutorial is meant to be used INTERACTIVELY; you may login to the CAOS/CAMM Center and run a GDB/OMIM session while reading the tutorial pages.

cc_news genomics

Please read the notices entered into cc_news genomics. We try to put information of relevance to users here, both specific to the CAOS/CAMM Center, and of a more general nature, such as announcements and postings to the various bionet newsgroups.

If you have anything you would like to broadcast to the genetics community, tell us about it! We'd be delighted to help you find the proper channels to your colleagues, known and unknown.

MultiMap Availability

We have had two requests for the chromosome mapping programme, MultiMap, to be made available to subscribers of the Genomics services. We have investigated the package and assembled the components required to get it running; you may expect it to be working by the middle of February, as well as an on-line (WWW version) tutorial, by early March.
Editor: Hens Borkent; WebMaster: Jack Leunissen