February 1996 - chemweb - imperial.ac.uk

Using Chemscape Chime
by h.rzepa＠ic.ac.uk 29 Feb '96

29 Feb '96

The way one can embed a chemical document within a HTML window is to use the following syntax; <embed border=0 src="halo.pdb" align=abscenter width=150 height=150 spiny=360 startspin=true display3D=ball&stick PLUGINSPAGE="http://www.ch.ic.ac.uk/cgi-bin/plugin.cgi"></embed> <noembed> <A HREF="halo.pdb"><IMG width=150 height=150 SRC="halo.gif" alt="chemical MIME"></A></noembed> Verious less obvious items need explanation; 1. The file halo.pdb returns the MIME header chemica/x-pdb from the WWW server. This instructs Netscape (the only browser to support plug-ins, although another is apparently on its way) to look for a plug-in supporting this MIME type. 2. The commands height=150 etc are recognised by the Chemscape Chime plug-in, which reads the file and produces an image. If two plug-ins both exists supporting the MIME type, they are resolved alphabetically (ie Chime would be used instead of e.g XMol) 3. If no plug-in exists in the plugins folder, control is passed to the following script; PLUGINSPAGE="http://www.ch.ic.ac.uk/cgi-bin/plugin.cgi which will provide information about the MIME types, etc etc. This works on a Mac, but I am not sure about Windows or Unix. 4. If the user is not using Netscape 2, the contents of <noembed> are displayed (Netscape 2 suppresses them), thus ensuring that something at least happens. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)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.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)

1 0

UK Mirror for MDLI's Chime Netscape PlugIn
by Dr Alan Mills 28 Feb '96

28 Feb '96

For those who still have difficulty getting hold of the Chime Netscape PlugIn from MDL Information Systems Inc's US site, we have put up a UK mirror for MDLI. It is at http://www.venus.co.uk/mdli/chemscape/chime/chime.html and includes a sample page with which to test the PlugIn, and screenshots of what it looks like in operation. This is an attempt to help overcome bandwidth problems experienced by people on this list, and should not be construed in any way as a product endorsement. Rgds., Alan Mills at Venus Internet Ltd, 24 Denmark Street, London WC2H 8NJ, UK email:alan@venus.co.uk web:http://www.venus.co.uk Tel: +44 (0)171 240 5858 Fax: +44 (0)171 240 5859 Providing Web and Internet services and solutions ----- 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)

1 0

Chime and External Helpers
by h.rzepa＠ic.ac.uk 27 Feb '96

27 Feb '96

The implications of using plug-ins are actually quite subtle and interesting. For example, MDLI Chemscape Chime has encoded internally some six chemical MIME types. When used as a plug-in, it appears to delete all these types from the options/general/helpers list that Netscape uses. The user does have the option of re-installing external helpers for chemical MIME, and these do take precedence over the plug-in definitions. What happens when for example two plug-ins both use the same MIME type is uncertain, largely because we have not yet found two plug-ins that address the same MIME type. The other aspect we are trying to resolve is that when the plug-in for a MIME type is not installed, and the HTML document references e.g a pdb file using an <embed> tag, Netscape invokes the following script; http://cgi.netscape.com/eng/mozilla/2.0/extensions/plugin.cgi?chemical/x-pdb Currently, Netscape have not implemented any info on chemical MIME, but when they do, some people might presume that this will act as the de-facto source of information on the topic. We are trying to find out if Netscape might be willing to put something useful to the chemical community into the response that http://cgi.netscape.com/eng/mozilla/2.0/extensions/plugin.cgi? produces. It is also possible to change the resource strings using an editor (such as ResEdit on a Mac) to redirect this to say; http://www.ch.ic.ac.uk/chemime/ but this runs the risk of contravening the Netscape license. We hope that the answers to these and other questions will be resolved shortly. If anyone has other thoughts/questions etc about the use of plug-ins in this context, do please send them to this list. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)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.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)

1 0

Chime Netscape plug in
by Stuart J. Fairall 23 Feb '96

23 Feb '96

If anyone wants a copy and indeed can place it somewhere more appropriate then a copy is available at:- http://www.dmu.ac.uk/~sfairall/chi08w95.exe Installs with a seamless no input installation. Hasn't made my Netscape 2/ Win 95 setup any slower or less stable than it was already. The Tags used to include it are simple and the embedded objects appear seamlessly and indeed due to the file sizes download faster than conventional graphics would. The display options available on the right click menu are reasonably comprehensive and the speed of response to changes in rendering is good. At present I cant quite see how to use RasMol as well and indeed cant even associate it again. When using it to view a standalone pdb file it seems to dislike resizing the window size and doesn't always update. Very interesting to see although rotating molecules on loading is a bit gee whizz. However how many people are using Netscape 2? I'm in the minority here and certainly our students won't be using it until it improves. ************************************************************** * Stuart J. Fairall * * sfairall(a)dmu.ac.uk * * http://www.dmu.ac.uk/~sfairall * * * * "If there was a GOD things like LIFE wouldn't happen." * * * ************************************************************** ----- 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)

1 0

Answers to some of the Questions about Chemscape Chime
by Bryan Van Vliet 22 Feb '96

22 Feb '96

I am the project manager for Chemscape at MDL. With regard to some of the questions regarding Chime(tm): * Do not download chi08w95.exe from www.dmu.ac.uk. This is an old version of Chime. We have addressed some of the initial problems discovered in this version (0.8), and have released Version 0.8a. Among the important problems we have fixed are installation failures and crash-related errors. You can download Version 0.8a, at our Web site http://www.mdli.com. We are also now providing a 16-bit version for Windows 3.1. MDL would like to have a mirror site on the other side of the Atlantic, but we would like to have the full set of Chime pages mirrored, which include an FAQ for using Chime. We will try to arrange this with one of the UK sites. * We are expiring Chime at the end of March because it is a prototype that we don't want floating around forever. We will be providing newer versions of Chime on our Web page and want users to move to them and avoid running into bugs which have already been fixed. Our intent is to make Chime free for academic users and personal use at home even for final versions. We also intend to make it free for commercial sites, but are struggling with the issue of how we would provide support services, which are important to companies. * This is a prototype (pre-Beta), and we do expect users to find problems. We plan to use the Web to provide updates as quickly as possible and address any problems. * We will be providing a Macintosh version as well as an SGI version. The Macintosh version is scheduled for completion by the end of April, but may be released (in prototype form) sooner. The SGI version is not due until early summer. * It will support TGF as well as 2D MDL Molfile and RxnFile. (There is a mistake in our FAQ regarding TGF support which I will correct.) We will be incorporating the necessary structure rendering code to do this in an upcoming version. * Netscape supports a NOEMBED tag which allows for an alternative to just displaying a blank page or "broken" plug-in image. We will have details on this in our FAQ, but just to be clear, the format is: <NOEMBED> HTML to be ignored </NOEMBED> For example: <EMBED SRC="sample1.rpm" WIDTH=300 HEIGHT=134> <NOEMBED> <A SRC="sample1.ram"> Play the audio using helper app! </A></NOEMBED> We appreciate all of the feedback on Chime and will strive to address any problems. Thank you. Bryan -- Bryan Van Vliet Project Manager, Internet Technologies MDL Information Systems, Inc. bryan(a)mdli.com 510.895.1313 x1160 ----- 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)

1 0

Re: Chime Netscape plug in
by jsb2＠camsci.com 22 Feb '96

22 Feb '96

>>However how many people are >>using Netscape 2? I'm in the minority here and certainly >>our students won't be using it until it improves. > >On our site, 49% of all browsers visiting are Netscape 2, 41% >are V 1.0, Mosaic is 2% and the rest nowhere. This is for >82000 hits over the last 10 days or so. Interestingly, 13% >were Windows-95, 32% Win-31, and 22% Mac. Interesting. On our site, from 10/Feb through 19/Feb, Netscape 2 was barely 33% of traffic. Netscape 1.x was about 47%. This is counting unique site-days: if one person looks at 10 pages, it counts the same as a second person looking at 1 page. MSIE figures excluded, of course. I think this is the most accurate way to measure browser distribution. What fraction of your users are local? I could see the numbers being skewed if, for example, Netscape 2.0 were readily available on a campus local server... Jonathan Brecher CambridgeSoft Corporation jsb(a)camsoft.com ----- 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)

1 0

Re: Chime Netscape plug in
by h.rzepa＠ic.ac.uk 22 Feb '96

22 Feb '96

>However how many people are >using Netscape 2? I'm in the minority here and certainly >our students won't be using it until it improves. On our site, 49% of all browsers visiting are Netscape 2, 41% are V 1.0, Mosaic is 2% and the rest nowhere. This is for 82000 hits over the last 10 days or so. Interestingly, 13% were Windows-95, 32% Win-31, and 22% Mac. I dont think Netscape 2 is a minority from this! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)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.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)

1 0

Re: Chemscape Chime
by h.rzepa＠ic.ac.uk 22 Feb '96

22 Feb '96

>X-Sender: wally(a)ng.netgate.net >Mime-Version: 1.0 >Date: Wed, 21 Feb 1996 15:15:50 -0800 >To: chemind-l(a)derwent.co.uk >From: "Walter E. Reiher III" <wally(a)CompChem.com> >Subject: Re: Chemscape Chime >Cc: h.rzepa(a)ic.ac.uk Someone in the States posted this; >I just downloaded and installed the demo and it looks _very nice_! However, >it appears there may be some problems in it--but then it is "prototype" code. > >It's an implementation of RasMol (MDLI says they're using Sayle's code) that >embeds interactive visualization windows in Netscape pages instead of using >a separate helper app. What's very nice about this is that one can view >interactive, rotatable images in, for example, HTML tables. MDLI has an >example: > > <http://www.mdli.com/chemscape/chime/sample.html> > >There are no 2D examples here, just nice looking 3D. > >I'm running it on a Windows NT 3.51 system, and this does work. Naturally, >I started to fiddle around with the images in this page (a .pdb file and 5 >.mol files), doing things like changing rendering styles just like RasMol. >Nice. Eventually, though, my NT system froze--something which happens very >rarely, and I push my system pretty hard. Seems like there are some >problems to work out but this is a very promising start! Definitely worth >downloading. > >Wally >======================================================================== >Walter E. Reiher III, Ph.D. Wally(a)CompChem.com >CompChem Innovations Consulting in computational chemsitry >P.O. Box 61056 voice 408-720-0240 >Sunnyvale, CA 94088 fax 408-720-0378 > Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)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.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)

1 0

Atlantic Bandwidth: Cans of Worms
by h.rzepa＠ic.ac.uk 21 Feb '96

21 Feb '96

Note: Repeat send. First one seems not to have gotten through. Apologies if you get this twice. ******************************* You may have noted a certain exasperation about the connection to the USA in my last message. I thought a few words on what I understand to be the current situation might help Two weeks ago, the existing Academic 4 Mbps link was due to be replaced by UKERNA, giving 9 Mbps. In order to install thee circuits, one of the two existing 2 Mpbs links was taken down. The last two weeks we have been operating on 2 Mbps to the USA. When they get the 9 Mbps up, UKERNA then plan (ie around mid March) to add further bandwidth, giving a total of 21 Mbps to the UK academic community. It is my understanding that potential users of e.g. SciFinder will need this bandwidth, since such client-server products rely entirely on such USA bandwidth. Quite what happens after that is unknown to me. Part of the problem is that this 21 Mbps is largely funded from UK sources. The original 4 Mbps link was equally funded from the USA and UK, being of course of benefit to both sides of the pond. As the USA moves more to "end user cost recovery", central funding from the USA side of things for the Atlantic link becomes less certain. Thus the 21 Mbps is NOT funded from the USA. It seems quite likely that further improvements will have to be funded by different mechanisms (this is purely my opinion). It may well be that some universities will decide to fund "private" links to the USA, and charge users for them. To quote Yogi Berra, in the midst of change, the future is not what it used to be. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)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.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)

1 0

First chemical Netscape Plug-in
by h.rzepa＠ic.ac.uk 21 Feb '96

21 Feb '96

MDLI have announced Chemscape Chime, a Netscape 2.0 plug in. Available currently only for Windows-95, I have not yet managed to get enough reliable Atlantic bandwidth to download the 800K .exe file. To quote " Chemscape Chime MDL's Chemscape Chime plug-in lets scientists display chemically significant 2D and 3D structures within an HTML page or table. Download Chime and then check out some Chime examples." >From this, I guess its a combined RasMol + ISIS/Draw working in-line on a Netscape page. See it at http://www.mdli.com/chemscape/chime/download.html If anyone manages to get all 800K across, do let us know what this product does! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa(a)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.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)

1 0