From gl@coil.mdy.univie.ac.at Thu Apr 4 05:20:45 1996 Received: from coil.mdy.univie.ac.at for gl@coil.mdy.univie.ac.at by www.ccl.net (8.7.1/950822.1) id EAA10191; Thu, 4 Apr 1996 04:54:04 -0500 (EST) Received: by coil.mdy.univie.ac.at (940816.SGI.8.6.9/930416.SGI.AUTO) id LAA01330; Thu, 4 Apr 1996 11:51:25 +0200 From: "Gerald Loeffler" Message-Id: <9604041151.ZM1328@coil.mdy.univie.ac.at> Date: Thu, 4 Apr 1996 11:51:23 -0600 In-Reply-To: smb@smb.chem.niu.edu (Steven Bachrach) "CCL:WWW developments" (Apr 3, 7:40am) References: <9604031340.AA08084@smb.chem.niu.edu> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: smb@smb.chem.niu.edu (Steven Bachrach), CHEMISTRY@www.ccl.net Subject: Re: CCL:WWW developments Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi! On Apr 3, 7:40am, Steven Bachrach wrote: > Subject: CCL:WWW developments > > I will probably get flamed for bringing up this subject as being too far > removed from comp chem but here goes.. > > I have been very impressed with a number of web developments like the Tripos > fetch and sketch, and the molecular inventor work of SGI. (If you missed the > demo of this at the ACS meeting, make sure to get your SGI rep or an MSI > rep to show it to you!). I would like to use the plug-in Chime from MDL, but > I'm not a windows user. > > Anyways, I would like to poll the community towards their attitudes and > desires in terms of how they would like to see chemical displays develop on > the web. The "old" technology was to provide a compound in one of a variety > of formats (pdb, xyz, etc), attach a MIME type, and then allow the user to > provide the molecular viewer locally (like Xmol or RasMol). With the > development of Netscape 2, we now have the Java option (like "fetch and > sketch") and the plug-in option (like chime). These latter options remove > the user from selecting the visualization tool. While this has advantages: > everyone now views the structure in the identical way, no need for the user > to have the appropriate viewer; it also removes the freedom to choose - what > if you don't like the Java applet provided? > > Before we all go and reinvent the wheel, and we have 30 different java > applets to rotate a molecule, can we discuss what's the "best" way to provide > the data to the general community? > > Steve > >-- End of excerpt from Steven Bachrach Here are my $0.02 on that subject: 1) Without doubt, the Java approach of having a Web-site publish the data _and_ the means (i.e., the applet) to view the data is the most intelligent solution to this whole problem area this far! 2) Nevertheless, I see two problems with that: a) It simply takes too long to download data+Applet every time you want to have a look at the data. b) While the Applet-approach potentially offers the possibility to publish every possible type of data (i.e., perfect freedom to choose on the publishers side) in practice, many pieces of data will still belong to one of the types already available as chemical MIME types. 3) A solution might be, to agree upon and develop _one_ set of Java-classes commonly needed by chemical data viewers: Handling PDB files, displaying and manipulating molecules, ... (in short: the handling and displaying of chemical MIME types.) This set will be useful to every Java-developer working in chemistry. As I understand Java, these classes could be stored locally (just like the classes being part of standard Java are), so that the process of repeatedly downloading them over the network is not necessary. Someone putting a PDB file on his Web-page just has to put a tiny Applet along with the data, that uses these standard chemical Java classes which would already be available on every chemists machine. Someone putting more sophisticated data on his page has to spice up his Applet with non-standard chemical classes, that would have to be downloaded over the net for every access to the data. Gerald -- Gerald Loeffler PhD student in Theoretical Biochemistry EMail: Gerald.Loeffler@mdy.univie.ac.at Phone: +43 1 40480 612 Fax: +43 1 4028525 SMail: University of Vienna Institute for Theoretical Chemistry Theoretical Biochemistry Group Waehringerstrasse 17/Parterre A-1090 Wien, Austria From tim@mdli.com Thu Apr 4 12:47:24 1996 Received: from one.mind.net for tim@mdli.com by www.ccl.net (8.7.1/950822.1) id MAA06080; Thu, 4 Apr 1996 12:17:48 -0500 (EST) Received: from nec.mentat.org ([206.101.74.4]) by one.mind.net (8.6.12/8.6.10) with SMTP id JAA29775; Thu, 4 Apr 1996 09:16:24 -0800 Message-Id: <2.2.32.19960404171843.00b25af0@mind.net> X-Sender: tim@mind.net X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 04 Apr 1996 09:18:43 -0800 To: chemistry@www.ccl.net From: Tim Maffett Subject: Re: CCL:WWW developments Cc: smb@smb.chem.niu.edu (Steven Bachrach) At 07:40 AM 4/3/96 -0600, Steven Bachrach wrote: > >I will probably get flamed for bringing up this subject as being too far >removed from comp chem but here goes.. > >I have been very impressed with a number of web developments like the Tripos >fetch and sketch, and the molecular inventor work of SGI. (If you missed the >demo of this at the ACS meeting, make sure to get your SGI rep or an MSI >rep to show it to you!). I would like to use the plug-in Chime from MDL, but >I'm not a windows user. Our Chemscape Chime Netscape Plug-In will also be available for SGI IRIX and Macintosh 68k/PPC. We are working with SGI to get the IRIX version available as soon as possible. > >Anyways, I would like to poll the community towards their attitudes and >desires in terms of how they would like to see chemical displays develop on >the web. The "old" technology was to provide a compound in one of a variety >of formats (pdb, xyz, etc), attach a MIME type, and then allow the user to >provide the molecular viewer locally (like Xmol or RasMol). With the >development of Netscape 2, we now have the Java option (like "fetch and >sketch") and the plug-in option (like chime). These latter options remove >the user from selecting the visualization tool. While this has advantages: >everyone now views the structure in the identical way, no need for the user >to have the appropriate viewer; it also removes the freedom to choose - what >if you don't like the Java applet provided? Chime 0.8b provides a 'Save' menu item which allows a user to save the molecule file to his local disk. From there the user can use his molecular viewer of choice to display the molecule. It is not MDL's intention to replace all molecular viewer technology with Chime, we are just trying to make it easy to have *some* way of viewing chemical structures withing a web page. Future versions of Chime will provide export type functionality which will allow the user to save the molecule file locally in various common molecule file formats, e.g., This will allow the user to view an XYZ file within a webpage, but save it locally as a MOLfile in order to read it into a program that only supports MOLfiles. > >Before we all go and reinvent the wheel, and we have 30 different java >applets to rotate a molecule, can we discuss what's the "best" way to provide >the data to the general community? > >Steve > >Steven Bachrach >Department of Chemistry >Northern Illinois University >DeKalb, Il 60115 Phone: (815)753-6863 >smb@smb.chem.niu.edu Fax: (815)753-4802 -tim From mgmsorg@bellatrix.pcl.ox.ac.uk Thu Apr 4 17:47:26 1996 Received: from oxmail3.ox.ac.uk for mgmsorg@bellatrix.pcl.ox.ac.uk by www.ccl.net (8.7.1/950822.1) id RAA11104; Thu, 4 Apr 1996 17:28:23 -0500 (EST) Received: from joule.pcl.ox.ac.uk by oxmail3 with SMTP (PP) with ESMTP; Thu, 4 Apr 1996 23:28:13 +0100 Received: from bellatrix (bellatrix.pcl.ox.ac.uk [163.1.21.231]) by joule.pcl.ox.ac.uk (8.6.10/8.6.5) with ESMTP id XAA09226 for <@joule.pcl:chemistry@www.ccl.net>; Thu, 4 Apr 1996 23:28:09 +0100 Received: by bellatrix (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id XAA00252; Thu, 4 Apr 1996 23:30:38 GMT From: mgmsorg@bellatrix.pcl.ox.ac.uk (mgmsorg) Message-Id: <199604042330.XAA00252@bellatrix> Subject: First Electronic Molecular Modelling & Graphics Society Conference To: chemistry@www.ccl.net Date: Thu, 4 Apr 1996 23:30:37 +0000 (GMT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text FIRST ELECTRONIC MOLECULAR GRAPHICS AND MODELLING SOCIETY CONFERENCE ******************************************************************** The First Electronic Molecular Graphics and Modelling Society Conference (MGMS EC-1) will be held on the Internet (the Net) and World Wide Web (the Web) from Oct 7-18, 1996. The conference is sponsored by Elsevier and the Molecular Graphics and Modelling Society and will be co-organized by Graham Richards, Art Olson, Rod Hubbard and Barry Hardy. MGMS EC-1 will be a fully international event open to all members of the scientific community and will cover a broad range of disciplines related to molecular modelling, graphics and simulation methods and applications. Conference subject areas are: Protein Structure; Membranes and Membrane Proteins; Bioinformatics; Computational Nanotechnology; Protein Folding; Modelling of In Vivo Activity; Knowledge-based Library Design; Surface Science; Host-guest interactions; Carbohydrates; Enzyme Mechanisms; Conformational Analysis; Nucleic Acids; Quantum Chemistry; Car-Parrinello Methods and Applications; Structure-based Design; Visualization; and Perspectives. Each subject area has a section convener who will screen abstracts sent by authors for suitability. Authors can opt to submit a non-permanent presentation like a normal conference poster or a presentation which will be refereed and considered for publication in the Journal of Molecular Graphics. Referees will be appointed by the section conveners. Presentations must be prepared in Hypertext Markup Language (HTML), graphics (GIF,JPEG) and other Web-compatible formats (VRML,Java,PDF) so that participants can view the papers via the World Wide Web. Aid and consultation will be provided to participants in the months prior to the event to help them with their presentation (Email:mgmsorg@bellatrix.pcl.ox.ac.uk). Further details will be given in the authors' guide accessible via the URL: http://bellatrix.pcl.ox.ac.uk/mgms/ During the conference discussions will take place via the Internet in real-time using a virtual conference centre based on a MOO (multiple-user domain, object oriented) and via Internet-accessible electronic mailing lists. Trial sessions for those not familiar with MOOs will be held before the conference. During the conference, a timetable for MOO discussion sessions of each section will be posted. Since these realtime discussions are an integral part of the conference, authors will be expected to attend one for their subject; the right is reserved not to referee submissions by authors who do not attend one of these sessions. The Conference will feature a Virtual Trade Center where commercial vendors, software and hardware developers, consultants, and contractors will be able to display their goods and services and provide software demonstrations in return for exhibition fees to support conference activities. Any potential exhibitors should contact Barry Hardy at barry@bellatrix.pcl.ox.ac.uk ******************* DEADLINES AND DATES 1) DO NOW - The MGMS mailing list Conference-related news and announcements will be posted regularly to the MGMS mailing list (http://bellatrix.pcl.ox.ac.uk/hypermail/mgms/). If you wish to subscribe to the MGMS list send the following one line message to majordomo@bellatrix.pcl.ox.ac.uk: subscribe mgms@bellatrix.pcl.ox.ac.uk your_email@address your_name 2) DO NOW - Registration The deadline for registration is Sept 15th 1996. Early registration is strongly encouraged to aid the efficient operation of the conference including the establishment of timely access to the conference. If you intend to participate in MGMS EC-1 please use the registration form accessible via http://bellatrix.pcl.ox.ac.uk/mgms/ which will be available for electronic registration starting April 22. The electronic registration will be used to construct a registrant database for the conference which will generate the conference mailing list and handle assignment of userids and passwords. In addition it is necessary to pay for registration via ordinary means: The conference fee will be 35 pounds sterling (50 US dollars) with a special rate for students of 20 pounds sterling (30 US dollars). A copy of a suitable student identification or a letter from the supervisor will be required to be charged at the lower rate. Cheques or bank orders (in pounds or dollars) should be made out to Greenlea Communications and mailed to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Please supply your complete name, address, fax and phone numbers, and email address in your correspondence. A conference userid and password will be forwarded to you. It is hoped to establish a credit card clearing service in May and information will be provided at the conference site in due course. Academic registrants from economically-disadvantaged countries can write to Barry Hardy requesting an exemption to the registration fee. Exemptions will be made on a discretionary basis taking into account the reasons given for the request and will be dependent on suitable funds being available. We will consider economically disadvantaged countries to include those of Eastern Europe, Africa, Central and South America, Indian sub-continent, etc. 3) DEADLINE for receipt of ABSTRACT. The deadline for receipt of presentation abstracts is July 1. Email your abstract directly to the appropriate section convener listed below. Fuller details of the scope of each section will be given in the authors' guide accessible via http://bellatrix.pcl.ox.ac.uk/mgms/ Your abstract should be no longer than 300 words. And remember to state which category of presentation (non-permanent poster or refereed paper) you wish. If you are unsure as to which section your abstract is suitable for, please email a possible section convener or Barry Hardy (barry@bellatrix.pcl.ox.ac.uk). Section conveners do have the discretion to reject abstracts, ask for revisions to an abstract or to send the abstract to the convener of a more suitable section. 4) DEADLINE for receipt of PRESENTATION The deadline for receipt of papers and posters is Sept 15th. You must deposit your text and graphics files at the conference ftp site for presentation at the conference. Ftp instructions are provided at the conference site. Hard copies of final refereed papers following the format of the Journal of Molecular Graphics should be sent by Dec 1 to: Graham Richards, Journal of Molecular Graphics, Physical & Theoretical Chemistry Lab, Sth Parks Rd, University of Oxford, Oxford, OX1 3QZ, UK. Journal guidelines will be posted at http://bellatrix.pcl.ox.ac.uk/mgms/ Although there is no limit to the graphics authors choose to display in their conference presentation, the editor reserves the right to limit the number of free colour figures in each printed journal article. 5) Refereeing Period The refereeing period will commence upon completion of the conference. If you have a presentation at MGMS EC-1 you may be requested to contribute a refereeing evaluation on another conference presentation. Referee reports will be due November 15. ******************* SECTIONS AND SECTION CONVENERS (Please email section conveners with questions related to your particular section and presentation. Details on the sections are accessible via http://bellatrix.pcl.ox.ac.uk/mgms/) Any general emails (such as registration queries, maillist queries, HTML queries, password queries, timetable queries, general technical advice on browsers and graphics, MOO queries, etc.) should be sent to: mgmsorg@bellatrix.pcl.ox.ac.uk 1. Protein Structure Rod Hubbard University of York, UK Email:rod@yorvic.york.ac.uk 2. Nucleic Acids David Beveridge Wesleyan University, USA Email:bever@rose.chem.wesleyan.edu 3. Membranes and Membrane Proteins Alan Robinson University of Oxford, UK Email:alan@bellatrix.pcl.ox.ac.uk and Terry Stouch Bristol-Myers Squibb, USA Email:stouch@dino.bms.com 4. Bioinformatics Convener to be announced Email:mgmsorg@bellatrix.pcl.ox.ac.uk 5. Computational Nanotechnology Al Globus NASA-Ames, USA Email:globus@nas.nasa.gov 6. Protein Folding Jeffrey Skolnick Scripps Institute, USA Email:skolnick@scripps.edu 7. Modelling of In Vivo Activity Edward Hodgkin Wyeth-Ayerst Research, USA Email:hodgkie@war.wyeth.com 8. Knowledge-based Library Design Mike Hann GlaxoWellcome, UK Email:mmh1203@ggr.co.uk 9. Surface Science Donald Brenner North Carolina State, USA Email:dwb@ripley.mte.ncsu.edu 10. Host-Guest interactions Jon Essex Southampton University, UK Email:J.W.Essex@soton.ac.uk 11. Carbohydrates and Protein-Carbohydrate Interactions Anne Imberty CNRS, France Email:imberty@nantes.inra.fr 12. Enzyme Mechanisms Guy Grant University College Dublin, Ireland Email:ggrant@macollamh.ucd.ie 13. Stochastic Methods for Conformational Sampling Robert Topper The Cooper Union, USA Email:topper@cooper.edu 14. Quantum Chemistry Tim Clark University of Erlangen, Germany Email:clark@organik.uni-erlangen.de 15. Structure-based Design David Winkler CSIRO, Australia Email:D.Winkler@chem.csiro.au 16. Car-Parrinello Methods and Applications Michele Parrinello Max-Planck Institute, Germany Email:prr@prr.mpi-stuttgart.mpg.de 17. Visualization Art Olson Scripps Institute, USA Email:olson@scripps.edu 18. Perspectives in Molecular Modelling Graham Richards University of Oxford, UK Email:gr@vax.ox.ac.uk