Instructions for Chemistry Authors

These instructions were made available to authors preparing articles for inclusion in ECHET96. They relate to the period around June 1996. Whilst much of these instructions remains relevant, some aspects have changed due to the availability of better software for the task. For a more recent set of instructions, please consult an on-line version available at the ECTOC-3 conference.

Authoring Tools

Microsoft Word, Wordperfect, PageMill, HotMeTaL or other HTML/RTF compliant Word Processor/Program (essential).
ISIS/Draw, ChemDraw, Chemintosh/ChemWindow or other program for creating structure diagrams (essential)
A HTML Editor (desirable).
A Graphical Image Editing Program (desirable).
Reaction Schemes in "tgf" format (optional).
Molecular coordinates in "molfile" or "pdb" format (optional).
Click here for a collection of useful programs.

Instructions on how to prepare an Article.

Conference Style.

All articles and posters will be mounted for the conference in the form of HTML (Hypertext-markup-language). The title should have a <H1> heading, the authors a <H2> heading and the address an <ADDRESS> heading. An example of how this might look is given below;

<center>
<H1> A Computational Model for Stereoselectivity in the 
Boron-Mediated Aldol Reactions of Methyl Ketones</H1>
<H2><A HREF="mailto:annab@iumchx.chimorg.unimi.it">Anna Bernardi</A>,(a) 
<A HREF="mailto:cesare@iumchx.chimorg.unimi.it">Cesare Gennari</A>,(a) 
<A HREF="mailto:jmg11@cam.ac.uk">Jonathan M. Goodman</A>,*(b) and 
<A HREF="mailto:ip100@cus.cam.ac.uk">Ian Paterson</A> (b)</H2>
<ADDRESS>(a) Dipartimento di Chimica Organica e Industriale,
Universita' di Milano, via Venezian 21, 20133 Milano, Italy<BR>
(b) <A HREF="http://www.ch.cam.ac.uk/">University Chemical Laboratory</A>, 
Lensfield Road, Cambridge CB2 1EW, England</ADDRESS>
</center>

At least one author should provide an e-mail address. You should include appropriate citations and diagrams, but take care not to 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.

Graphical Abstract: Each article will have a small graphical abstract in the titles page. This will be precisely 196 pixels wide and 64 high. Authors were asked to provide this if possible in "GIF" format. We asked that this graphical abstract be given the name ga.gif. If no diagram is provided, the editors selected one from the material provided.

Author Expertise

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

Non-Hypertext Author Mode: (Word Processor Documents) The article should be prepared using a standard word processor; Microsoft Word is the preferred choice if possible. Diagrams should be pasted into the word processor, the document saved in Microsoft Word Format or in "interchange or RTF" format. and submitted as described here. 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 article or poster.
Recommended Author Mode:(HTML Documents) A word processor document can be prepared as described above. A wide variety of Word Processors now support HTML as an output format, including Microsoft Word (via Internet Assistant), WordPerfect, Claris Works, PageMaker, etc. If you want to "fine-tune" the HTML saved in this way, a general beginners guide is available. A concise set of commands is available here. Alternatively, you can view the HTML source for this and other documents by selecting View source within Netscape or other browser and learning by example.
Commercial programs such as HotMetaL Pro from SoftQuad, PageMill from Adobe or Netscape Gold can be used as an alternative to a Word Processor. The advantages are that graphical handling is done automatically. In particular, you should try to ensure that the conference style is followed if possible.
Naming of documents
We advise following the following guidelines regarding names of any HTML documents

The main page of the article or poster, containing if needed links to other documents, should be named if possible index.htm
It is helpful to keep names to 8 characters in length (for backward compatibility with DOS users), although not essential (since Windows 95 now accepts long names).
Please do not use spaces in names (a Macintosh allows this) because the Unix based server will not accept them.
Advanced Author Mode: (HTML Documents with Hyperlinks) 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. 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. A suitable free editor on a Macintosh computer is BBedit Lite, for which a number of so-called HTML extensions are available. Using these, entries in the HTML document of the type <A HREF="atp.pdb">here is an active molecule</A> can be inserted. A complete environment for Windows users is HotDog Pro.
Types of Hyperlink.

<A HREF="part2.html">connection to another HTML document</A>.
<A HREF="diagram.gif">connection to a diagram</A>.
<A HREF="molecule.pdb">connection to 3D Molecular coordinatest</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 images seen in a Netscape document window can be acquired for your own use by an extended mouse press which brings up a menu which enable you to copy the image to the clipboard.
Graphical Images

Image Files. Image files are handled separately from HTML documents, although they must be called from within the latter. The most popular format for saving the image files is in "GIF" mode. Some commercial authoring programs will directly produce files in this format (e.g. HotMetaL Pro, PageMill), whilst others produce intermediate format files (Microsoft Word for Windows produces "wmf" or Windows Meta-File format graphics; on a Macintosh these are normally "PICT" files, as produced for example by the rtftohtml program). A Macintosh shareware program called GraphicConverter can be used to convert to GIF format and additionally to apply so called "transparency" to your image, to change colours, re-scale, add captions, and 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 (or transfer slowly across a congested Atlantic link!). In general, rescaling large images does not work well, since any text embedded in them 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. Take care when saving an image that it is not saved at > 100 dpi resolution (which can sometimes happen in ChemDraw, where PICT images can be saved at 300 dpi. In general, rescaling a bitmap image back down to e.g. 72 dpi produces unsatisfactory results.

Reaction Schemes as TGF Files
A standard format for saving structure diagrams or reaction schemes is the MDL TGF format, currently supported by the ISIS/Draw program. ChemDraw Pro (3.5) also supports the TGF format as an inport/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 article/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 article 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.

Draw the structure diagram using a suitable structure drawing package, save the diagram as a GIF file (or PICT if GIF format is unavailable and then convert to GIF. ChemDraw has a script that does this; ChemWeb will do this directly). It helps to colourise the anticipated hotspots to help readers identify them. For illustration, lets call the diagram scheme.gif
Create a small dummy HTML document with the single entry;
<A HREF="dummy"><IMG SRC="scheme.gif" ISMAP></A>and open this file with Netscape 2.0. As you pass the cursor over various regions of the file, Netscape 2.0 will display the pixel coordinates of the cursor. Note the top left, and bottom right X and Y positions of the "hotspots" you wish to mark (only rectangular areas are currently supported).
Create HTML entries of the following type, where the coordinates are entered in the order noted above;

<MAP NAME="mapname"> <AREA SHAPE=rect COORDS="10,12 202,240" HREF="molecule.pdb"> <AREA SHAPE=rect COORDS="209,12 422,240" HREF="experimental.html"> <AREA SHAPE=default HREF="scheme.gif"> </MAP> <A HREF="http://www.ch.ic.ac.uk/cgi-bin/imagemap/mapname"> <IMG SRC="scheme.gif" USEMAP="#mapname" ISMAP></A>

The hyperlinks 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. The above syntax will serve two functions. When inserted into an HTML document viewed by Netscape 2.0, "local" resolution of the mapping will occur, and you can test the map yourself. If this document is viewed by a Web Client which does not support "local" mapping, then the imagemap program on the ECHET96 server will attempt to do this. The conference editors will set this up from the HTML you provide.

"Hyperactive" Molecules: Chime™and VRML
We positively encourage authors to submit molecular coordinates derived from crystallographic or modelling studies. The preferred format is the Brookhaven "pdb" or MDLI Mlfile 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. You will also need to install the Chime™browser plug-in to take advantage of this mode of presentation. The syntax you will have to insert into your HTML code is as follows;
<embed border=0 src="atp.pdb" ALT="ECHET96" align=abscenter width=150 height=150 spiny=360 startspin=true display3D=ball&stick name="echet96"> <noembed><A HREF="atp.pdb"><IMG border=0 width=97 height=77 ALT="ECTOC Conference Series" SRC="echet96m.gif"></A></noembed>
You can also use CSML (Chemical stucture markup language) to highlight individual atoms or groups in the molecule. Insert something like the following into your HTML;
<font COLOR="#0000FF">functional group transform</font> <embed src="atp.csml" width=12 height=12 target=echet96 button=push (click button on left).
Finally, you will have to create a file called e.g. atp.csm which might contain the following;

all cpk wireframe on atomno=10 blue spacefill on atomno=26 orange spacefill on
If this is placed on your own server, make sure that the following MIME type is defined on your server;
chemical/x-csml csml, csm
This would produce the effect;
key features highlighted (click button on left).
You may also wish to provide 3D coordinates in the form of VRML files. These have the advantage that you can insert "hyperlinks" directly associated with individual atoms, bonds, or regions of the molecule. VRML can also be used to display computed properties of molecules such as orbitals, various surfaces, etc. The following syntax;
<embed src="dmso4.wrl" width=100 height=100>
wll enable a VRML encoded file to be included. A VRML plug-in such as Live3D comes as a component of the Netscape Installer.
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.

Tabular Data
You are encouraged to present tabular material in HTML table markup. An 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 alt="two" 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 alt="one" 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

Semi-empirical Ab initio

1.9 3.1 A.Body, J. Am. Chem. Soc., 1996, 222.

5.8 6.2 N.O. Body, J. Perkin Trans., 1998, 222

Authoring programs such as HotMetaL Pro 2.0, PageMill etc can prepare tables automatically for you. There are also programs that will read Excel spreadsheet files and convert these to tables.
Superscripts, Subscripts, Non-standard and Greek Characters
The markup for superscripts and subscripts is as follows; H<sub>2</sub>O<sup>+</sup> to achieve the effect H₂⁺.
A partial selection of non-standard characters is supported by the Netscape browser entering the string &#number code;

            

‚ 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

To insert Greek characters, use the following syntax;
<FONT face=symbol>a,b,g</font> to achieve the following effect;
a,b,g
Documents with Multiple Windows
Netscape 2.0 allows you to use the browser window to display two or more documents simultaneously. One document can be used for e.g. navigation and will always remain visible, whilst a second can display the article or poster. This can be achieved using the following construction;
<HTML><HEAD><Title></title></HEAD> <FRAMESET ROWS="75,*">  <NOFRAMES> <BODY> Material that will only be seen by Browsers that do not support multiple windows </BODY> </NOFRAMES> <FRAME SRC="static_window.html" NORESIZE NAME="static"> <FRAME SRC="main_window.html" NAME="main" scrolling=yes> </FRAMESET> </HTML> <HTML><HEAD><TITLE>static_window.html</TITLE></HEAD> <BODY> <center> <A HREF="part1.html" target="main">Results</A> <A HREF="part2.html" target="main">Experimental</A> </BODY> </HTML> <HTML><HEAD><TITLE>main_window.html</TITLE></HEAD> <BODY> Introduction </BODY> </HTML>

Support for Java
Java is not used in the conference proper, but may be incuded in the CML section.
© ECHET96. February, 1997.

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