Index

Tools for Writing a Paper or Poster

Microsoft Word, Claris Works, Wordperfect or other HTML/RTF compliant Word Processor.
ISIS/Draw 1.2w or other program for creating structure diagrams.
A HTML Editor (optional).
A Graphical Image Editing Program (optional).
A Program for 2D Image Mapping (optional).
Reaction Schemes in "tgf" format (optional).
Molecular coordinates in "molfile" or "pdb" format (optional).
Microphone and software for recording audio clips (optional).

Instructions on How to prepare a Paper.

According to your experience with computers and preparing electronic documents, we envisage three levels of paper or poster preparation.

Non-Hypertext Author Mode.

The conference paper style should follow the style of e.g. Synlett, Chemical Communications or Perkin Transactions, with appropriate citations and diagrams. We also recognise that this is a new medium, and are happy to accept experimentation from authors. For example, posters could be prepared as one or more reaction scheme diagrams using a suitable program, linked if necessary with suitable headings and captions written using a word processor. Do not make any diagram larger than a standard 14" computer monitor is capable of displaying in its entirety. Users of large (> 19") monitors should be particularly wary. Diagrams should be pasted into a Word Processor and in either case, the resultant Microsoft Word/Claris/WordPerfect File should be saved as "rtf" or "interchange format" and sent as an e-mail enclosure to ectoc-contrib@ic.ac.uk, or written to a 3.5" 800/1.4M floppy PC or Macintosh formatted disk and sent to:
ECTOC Department of Chemistry Imperial College London, SW7 2AY. Documents submitted in this manner will be converted to "hypertext" by the conference editors, but we cannot guarantee that the original word processor layout can be fully preserved or that any hypertext links or other more advanced features will be included in the final paper or poster.

Recommended Author Mode:

A Microsoft Word/Claris/Wordperfect document should be prepared as described above. You have the option of saving the document as a "rich text format" RTF file (also described as Microsoft Interchange format) for subsequent conversion to HTML. Alternatively, you can acquire specific tools to add to your word processor and add any hypertext elements to your paper or poster directly. If you want a general primer on the language, several beginners guides are available. Alternatively, you can view the HTML source for this and other documents by selecting View source within Netscape 1.1N or other browser and learning by example.

PC Windows Users: The preferred word processor is Microsoft Word 6, for which "Internet Assistant" or QuarterDeck Tools are available. Wordperfect users can use Internet Publisher for WordPerfect . All are currently in beta test. Internet Assistant will NOT convert any graphical images in your document, and Microsoft suggest you process these separately using e.g. Microsoft Imager or other 3rd party software.
You may also wish to consider using either a custom template for Word or an RTF conversion program known as rtftohtml, which have been around longer than the Microsoft product. The latter program WILL convert graphical images, into the so called "wmf" or Windows Meta-Files format graphics. You will need to convert these into the "gif" or "JPEG" formats used in Netscape. If you have no suitable program, then these files should be sent to the conference editors for conversion.
Macintosh Users: Microsoft have announced that Internet Assistant will be available for Macintosh Word 6 in mid summer 1995, which is too late for use in ECTOC. The currently preferred route is therefore to save the document as an RTF file and pass this through "rtftohtml". In selecting a file name for the RTF, try to chose one which stands a good chance of being unique, and give it a .rtf suffix (e.g. blogs-smyth.rtf). The current version of rtftohtml will automatically cope with superscripts and subscripts. Only a limited selection of Greek symbols is available which will have to be edited in by hand. The output of rtftohtml comprises a sequence of files of the type;
```
blogs-smyth.html
blogs-smyth_ToC.html
blogs-smyth_fn.html
blogs-smyth1.PICT
blogs-smyth2.PICT
```
...
If you use Claris Works, you can use a special HTML XTND Filter to save directly as HTML and PICT files.
The final task is to convert all the graphic files produced by the filters noted above from PICT to GIF format. A shareware program called GraphicConverter can be used to do this, and additionally to apply so called "transparency" to your image, to change colours, re-scale, add captions, etc. Remember to save your image files in the GIF or JPEG formats. Just for the record, this program will also convert from a large variety of other graphical formats, including the Windows Meta-Files format noted above, Silicon Graphics "rgb" format and many others.

Advanced Author Mode:

The true benefits of authoring HTML documents will only come when hyperlinks to other documents, "hyperactive" molecular diagrams and other more advanced components are included. Adding hyperlinks can in fact be done directly using advanced word processors such as Microsoft Word and tools such as Internet Assistant or custom Templates. By following certain simple instructions it is also possible to insert hyperlinks using the standard version of Word, ready for conversion into HTML by rtftohtml. The most direct way of inserting hyperlinks is by using an appropriate text editor operating directly on the HTML file, which how all these pages were created. The recommended editor on a Macintosh computer is BBedit, for which a number of suitable so-called HTML extensions are available, including "anchor", "style", "heading", "preview" and "utilities". Using these, entries in the HTML document of the type <A HREF="atp.pdb">here is an active molecule</A> can be inserted. The equivalent tool on Microsoft Windows is HTML Hyperedit.

Advanced Tools

HotMetaL is a HTML editor which also checks the syntax of your markup.
SGI also market a complete system called WebForce.
A new product called arachnid offers a compositional tool which allows a Web page to be composed interactively. This might be appropriate for creating posters and other pages with more complex layout.

Types of Hyperlink. Internet resident material can be referenced in the following ways;

<A HREF="mail/">connection to a WWW document</A>. You might wish to insert hyperlinks to e-mail messages relevant to your paper in the final revision.
<A HREF="gopher://gopher.ch.ic.ac.uk/">connection to a Gopher document</A>
<A HREF="ftp://ftp.ch.ic.ac.uk/pub/">Connection to an anonymous ftp server</A>
<A HREF="telnet://argon.ch.ic.ac.uk">Connection to a terminal service</A>
<A HREF="mailto:rzepa@ic.ac.uk">Link for sending an e-mail message</A>. It is suggested that you insert your e-mail address in this manner so that conference editors and others can more easily contact you.

You can also easily acquire such "URL"s by selecting the string in the location window of the Netscape browser and copy/pasting it into your own document. Similarly, any text (but not images) seen in a Netscape document window can be acquired for your own use, as for example literature citations, numerical data etc.

Graphical Images, Sounds and Animations

Images. Graphical images to be referenced in the HTML document should normally be in GIF format, although the JPEG format is also accepted. A shareware program to convert Macintosh PICT to GIF files is available which can operate in "batch" mode, i.e. convert all your images in a single pass. This program can also process a huge variety of other graphical formats.
Guidelines for Preparing Images. The most important advice is to avoid preparing large images that will not fit onto the screen of standard (14") monitors. This can be only to easy to do if your own monitor is 19". In general, rescaling large images does not work well, since any text can become unreadable. Chemical structure diagrams are normally created as monochrome images. Sometimes however, a little colour helps to clarify the points. In general, 8-bit colour is used in the GIF format. Exceptionally, you might wish to use more colours, such as when relying on depth cueing or shading of say protein structures, and only the JPEG format will support this. Avoid using colours which will be indistinguishable on monochrome monitors.
Postscript files are not acceptable, although we are prepared to consider the "distilled" Adobe Acrobat (pdf) format if it is hyperlinked to an abstract of the paper submitted in HTML.
Sounds and Animations. Sound files in "ulaw" format introducing papers or elaborating other points are welcome. These can be readily produced using the Microphone accessory on Macintosh computers and the Sound Machine program. Suitable software for PC systems fitted with sound cards is also available. Video animations in MPEG or Quicktime are also supported, but files larger than 500K are not encouraged. The arcane art of producing movies is somewhat too complex to describe here.

Reaction Schemes as TGF Files

A standard format for saving structure diagrams or reaction schemes is the MDL TGF format, currently supported by the freely availableISIS/Draw 1.2w program. ChemDraw Pro (3.5) also supports the TGF format as an export option. Inserting a hyperlink within your text to a TGF file, as for example;
The synthetic sequence is described in <A HREF="s1.tgf">scheme 1</A>
will allow the reader of your paper/poster to acquire a "live" scheme which they can use locally. Schemes in TGF format can also be included as e-mail enclosures. Any TGF files should be included with HTML and other files in your paper or poster submission. To see some examples of the use of TGF files, connect here.

Creating Reaction Schemes with Hyperlinks

It is also possible to produce complex reaction schemes with embedded hyperlinks to e.g. reagents used at each step, perhaps crystallographic coordinates of key intermediates, explanations of functional group transforms etc. If you wish to try creating such a diagram or poster, proceed as follows. The following explanation relates directly to the use of Macintosh computers, although similar programs are also available for PC.

Draw the structure diagram using a suitable structure drawing package and save the diagram as a PICT file rather than as TGF. It helps to colourise the anticipated hotspots to help readers identify them.
Acquire a program called WebMap and read the PICT file into this.
Select either a rectangular or circular "hotspot" marker. For each hyperlink, you will be asked to provide a "URL" reference. This can be either to a HTML file containing e.g. reagents, or explanations of functional group etc, or to a PDB coordinate file or any other sources of relevant information. When finished, "export" the map file, giving it a name with a .map suffix. You will be asked to provide a "default" URL, which can be left blank.
The final step is to convert the PICT file to GIF format, using GraphicConverter or other suitable program. All the relevant HTML files, the MAP and the GIF files should be submitted as your contribution to the conference. The conference editors will add the MAP reference to the server.

"Hyperactive" Molecules

We positively encourage authors to submit molecular coordinates derived from crystallographic or modelling studies. The preferred format is the Brookhaven "pdb" format for 3D data. Coordinates provided by most crystallographers normally come in SHELX format. You should ensure that when the SHELX file is created, the crystallographer writes out complete molecular coordinates, and not just the unique "asymmetric" atoms. Conversion of SHELX to PDB can be accomplished using SHELX93, Chem3D or Babel.

The "official" conference 3D molecular viewer is RasMol/RasMac. Alternatives are Chem3D Viewer. Reference to PDB coordinate files can be made as "hyperlinks" in the HTML text prepared from the original word processed paper. For example, a link of the type <A HREF="atp.pdb">Click Here to see molecule</A> will enable the transfer of coordinates to the user and result in activation of the RasMol program automatically. In order that these types are automatically recognised, please ensure that the filename suffix is .pdb. Check also that your World-Wide Web browser is suitably configured.

X-Ray Data

If you have x-ray data associated with any structures that you would wish to deposit with the Cambridge data centre, a set of instructions to help you has been prepared. Click here for further details.

Other Types of Active Molecular Data

If authors wish to submit spectral data, we suggest that the original spectrum is scanned and saved as a GIF format image. We are currently investigating the JCAMP-DX format for viewing NMR, MS and IR data, for which a Windows based viewer is available.

Tabular Data

A table prepared in e.g. Microsoft Word will be translated into so called "pre-formatted" text when converted to HTML markup. If a more complex representation is required, two options are available.
(i) A "screen-dump" of the original Word table can be taken, and converted to a GIF graphic image, to be included in the final HTML markup.
(ii) The tabular material is converted to HTML table markup. An example of how the table for the special character set below was set up can be obtained by saving the source HTML for this document. A more complex example, including hyperlinks and images is as follows;

<table border>
<caption><b>Table 2. Calculated Isotope Effect</b></caption>
<tr><th rowspan=2>System</th><th colspan=2>Method</th><th rowspan=2>Literature<br>reference</th></tr>
<tr><th>Semi-empirical</th><th><I>Ab initio</I></th></tr>
<tr><td align=left><A HREF="dummyentry"><IMG SRC="struct1.gif"></A></td> <td>1.9</td> <td>3.1 </td><td>A.Body,<I> J. Am. Chem. Soc.</I>, 1996, 222.</td></tr>
<tr><td align=left><IMG SRC="struct2.gif"></td><td>5.8 </td><td>6.2 </td><td> <A HREF="http://machine/paper.html">N.O. Body,  <I>J. Perkin Trans.</I>, 1998, 222</a></td></tr>
</table>

Which gives the result:

**Table 2. Calculated Isotope Effect**
System	Method		Literature reference
System	Semi-empirical	Ab initio	Literature reference
	1.9	3.1	A.Body, J. Am. Chem. Soc., 1996, 222.
	5.8	6.2	N.O. Body, J. Perkin Trans., 1998, 222

Superscripts, Subscripts and Greek Letters

The markup for superscripts and subscripts is as follows; H<sub>2</sub>O<sup>+</sup> to achieve the effect H₂⁺. Only the NCSA Mosaic browser (2.00b12 or later) currently supports this construct. A partial selection of Greek characters is supported by the Netscape browser (V1.1N) or Mosaic 2.00b12 by entering the string &#number code;

**Character Entities in Netscape 1.1N or Mosaic 2.00b12**

‚	ƒ	„	…	†	‡	ˆ	‰	Š	‹	Œ		Ž

		‘	’	“	”	•	–	—	˜	™	š	›
		¡	¢	£	¤	¥	¦	§	¨	©	ª	«
ž	Ÿ	¡	¢	£	¤	¥	¦	§	¨	©	ª	«
¬		®	¯	°	±	²	³	´	µ	¶	·	¸
¬		®	¯	°	±	²	³	´	µ	¶	·	¸
¹	º	»	¼	½	¾	¿	À	Á	Â	Ã	Ä	Å
¹	º	»	¼	½	¾	¿	À	Á	Â	Ã	Ä	Å

You will probably find that different computers might display different characters to these, a major outstanding problem in HTML. We expect a full set of Greek symbols to be supported with future releases of browsers and HTML.

Instructions on How to Submit a Paper.

Once your material is prepared, you can submit it to the conference in several ways.

Ask a local "Webmaster" to mount your HTML files without further modification on a local server, and send the URL of the title page to ectoc-contrib@ic.ac.uk.
Send the collection of files to the conference editors by creating a single "archive" file in "ZIP", "COMPACT Pro" or "Stuffit" formats and attaching this to an e-mail message sent to ectoc-contrib@ic.ac.uk. Remember to suitably encode the archive first (ie as uuencoded or binhexed files). The Eudora mailer will do this for you.
Send the collection of files to the conference editors by creating a single "archive" file in "ZIP", "COMPACT Pro" or "Stuffit" formats and transferring the archive to the anonymous ftp server ftp.ch.ic.ac.uk in the directory ectoc. Log into the server as anonymous and supply your e-mail address as the password. You MUST notify the conference editors that you have done this by sending a message to this effect to ectoc-contrib@ic.ac.uk.
Write the complete collection of files to a PC or Macintosh formatted floppy disk and send to;
ECTOC Department of Chemistry Imperial College London, SW7 2AY.

Internet Connections

The expression "Internet ready" implies a computer which is either permanently connected to a network, or which can be connected temporarily using a Modem or other communication device. Because the precise details vary according to the type of computer, and the form of software implemented, it is virtually impossible to set out here how the entire task might be accomplished. Perhaps the best advice is to consult a local network expert, who will in any case also be aware of other local issues such as security, "firewalls" and other arcane aspects. Further details can be obtained from; "Chemical Applications of the Internet", Ed. S. Bachrach, ACS Publications, 1995.

Serving your own Papers

If you have a WWW server running locally, you can mount your material there, and send just the "URL" to the conference editors. Your local "Webmaster" should have all the details of how to do this. There are only a small number of "non-standard" features which you will have to ask the Webmaster to implement. These relate to MIME types for molecular coordinate files (if you are using them). Two (or more) entries will have to be added to the server configuration file. If you are using the NCSA Server, ask for the following two lines to be inserted into the mime.types file on the server;

chemical/x-pdb            .pdb
chemical/x-mdl-molfile    .mol
chemical/x-mdl-tgf        .tgf

If your site runs the CERN server, the following has to be inserted into the httpd.conf file;

AddType         .pdb            chemical/x-pdb          7bit            1.0
AddType         .mol            chemical/x-mdl-molfile  7bit            1.0
AddType         .tgf            chemical/x-mdl-tgf      7bit            1.0

The chemical MIME type is in the process of being formally proposed, and hopefully eventually ratified. Whilst this process is occuring, the "x" in the above entries signifies an unratified standard. Some time after June 1995, we expect that the "x" designation will be removed, but its use will be assumed for the ECTOC-1 conference.

Other HINTS: Because many people across the world may wish to contact your server, please have regard for the possibility that their network connections may be quite slow. For example, a HTML file of more than about 25 Kbytes may take a long time to transfer, as would a large number of GIF images. If possible, split your documents into many small ones, with an index page that contains all the relevant information.


‚	ƒ	„	…	†	‡	ˆ	‰	Š	‹	Œ		Ž

		‘	’	“	”	•	–	—	˜	™	š	›
		¡	¢	£	¤	¥	¦	§	¨	©	ª	«
ž	Ÿ	¡	¢	£	¤	¥	¦	§	¨	©	ª	«
¬		®	¯	°	±	²	³	´	µ	¶	·	¸
¬		®	¯	°	±	²	³	´	µ	¶	·	¸
¹	º	»	¼	½	¾	¿	À	Á	Â	Ã	Ä	Å
¹	º	»	¼	½	¾	¿	À	Á	Â	Ã	Ä	Å


‚	ƒ	„	…	†	‡	ˆ	‰	Š	‹	Œ		Ž

		‘	’	“	”	•	–	—	˜	™	š	›
		¡	¢	£	¤	¥	¦	§	¨	©	ª	«
ž	Ÿ	¡	¢	£	¤	¥	¦	§	¨	©	ª	«
¬		®	¯	°	±	²	³	´	µ	¶	·	¸
¬		®	¯	°	±	²	³	´	µ	¶	·	¸
¹	º	»	¼	½	¾	¿	À	Á	Â	Ã	Ä	Å
¹	º	»	¼	½	¾	¿	À	Á	Â	Ã	Ä	Å


‚	ƒ	„	…	†	‡	ˆ	‰	Š	‹	Œ		Ž

		‘	’	“	”	•	–	—	˜	™	š	›
		¡	¢	£	¤	¥	¦	§	¨	©	ª	«
ž	Ÿ	¡	¢	£	¤	¥	¦	§	¨	©	ª	«
¬		®	¯	°	±	²	³	´	µ	¶	·	¸
¬		®	¯	°	±	²	³	´	µ	¶	·	¸
¹	º	»	¼	½	¾	¿	À	Á	Â	Ã	Ä	Å
¹	º	»	¼	½	¾	¿	À	Á	Â	Ã	Ä	Å