Eventually, we should come up with some nice format for articles about chemical compounds. Right now, I like caffeine: a picture of the 3-d structure, a picture of the chemical structure, the chemical formula and the correct name. Maybe the CAS number should be added for completeness. I know that 3-d structure images can be produced with the program rasmol. Does anyone know a nice program for producing the 2-d structure formulas? Right now, I use JChemPaint and I don't like it. AxelBoldt 03:36 Dec 17, 2002 (UTC)
I've used molpov before. its pretty cool. it takes a .mol file and creates 2d or 3d POV renderings out of them. its really powerful and slick. but you do needa POV program for it to work (I use PovRay) both of those are freeely available. either frreeware or maybe even Free Software, I don't remember at the moment. Lightning 22:41, 13 Aug 2003 (UTC)
The 3D picture on caffeine is way too dark -- I can't see much at all on my monitor. A lighter background would be better -- grey, or the same shade of cream as the 2D diagram. -- Tarquin (but apart fomr that, caffeine is good. I've been editing articles on compounds to open with:
Discussion of the table for inorganic compounds given at Inorganic table information should probably take place here... AxelBoldt 23:04 22 May 2003 (UTC)
Has any consensus been reached on how to name articles describing chemical compounds. Obviously, there are cases where the systematic name for the compound is not the appropriate name for the article. An extreme example would be water. And since the sort of chemicals that are of sufficient industrial, historical, or pharmacological importance to merit articles are exactly the sort of compounds likely to be better-known known by a common name than their systematic one, I guess, how should we decide? Take the Google poll? Use whatever comes first in a standard reference like the Merck index? Any other thoughts?
Shimmin 04:14, 22 Aug 2003 (UTC)
Have it both ways. Redirect
Usually I would have the trivial name as the primary page, since that's what most people will be searching on if they don't know much about it - unless the trivial name is actually obsolescent. Have a redirect from the IUPAC name if it's reasonably compact and likely to be easy to type without errors. For the really hard IUPAC names, they might just have to rely on the search function - which implies all chem pages should include the IUPAC name in the text. -- Roger 10:08, 03 Sep 2003 (UTC)
Chemical Structure Program
Can anyone recommend a decent free program that draws chemical structures. One that's not too hard and runs under Windows or Linux would be great. ThereIsNoSteve 05:29, 29 Sep 2003 (UTC)
One program is xymtex, that someone has used to do the steroid hormones. e.g. Image:Testosterone.png. I've never used it, so i can't tell you anything about it. I guess it's similar to Latex etc. (haven't used that either) Tristanb 06:04, 29 Sep 2003 (UTC)
I searched around for a while and the best I could come up with was ChemSketch; it's freeware for Windows, but not open source. In the long run, we need (and will certainly get) something like our wikipedia:TeX markup feature which would allow you to specify a molecule structure in TeX and it's typeset automatically. AxelBoldt 16:47, 29 Sep 2003 (UTC)
I agree about the TeX. There a whole lot of (La)Tex packages out there that support typesetting technical things like chemical structures, syntax trees, mathematical plots, Feynman diagrams, phonetic symbols, Karnaugh maps, etc, that would otherwise have to just be made by hand and uploaded as an images. The downside of this is that there is nothing ensuring consistency in style of the diagrams, and modifying the bitmaps is non-ideal. Being able to edit the TeX source, while not extraordinarily easy, would be more in keeping with wiki style. Plus, if we get really clever, we could generate higher-resolution versions for print pages. Before I got sucked in to the whole logo-debate and modifications, I was working in the background on modifying the TeX support in MediaWiki to support phonetic symbols, but it seems abstracting it to support a variety of packages would be the best solution. On the other hand, SVG images for a lot of this stuff would probably be better. -- Nohat 18:05, 29 Sep 2003 (UTC)
Personally, I use ChemSketch (I forget the site). You can make images out of the chemical structures simply by copy pasting from ChemSketch to your favorite image program (such as IrfanView or Paint). Certain things don't work, though (including phosphate groups, I couldn't make the structure for ATP because of that). ugen64 20:04, Nov 22, 2003 (UTC)
ISIS Draw is not open source or any such, but is not bad for a windows box. Personally, I use the entirely-not-free CS Chemdraw - it is the best by some way. Iridium77 17:44, 23 Feb 2004 (UTC)
If consistency of style is important, the ideal solution would be to have the wiki-code be a SMILES string, from which an onsite application would generate a chemical structure. ChemDraw does this, and there is at least one applet on the web that does it. I have no idea what would be involved in coding up such a function for the wiki, though. Shimmin
That's okay for simple stuff, but for anything more complicated, it becomes irritating to not be able to define the orientation that you actually want in the diagram. For some things, it's impossible: try getting any app to draw a metallocene legibly from SMILES :-)
I've done many structures with PPCHTeX, like nicotine, omeprazole and fluphenazine. I don't know what you think about it; when it works, it works, but I suspect there are more flexible methods that work in all cases. [[User:Sverdrup|❝Sverdrup❞]] 23:20, 15 Aug 2004 (UTC)
Unless anyone objects, the standard wikipedia symbol for equilibrium will be ↔, until someone fixes this problem. Resonance will need another symbol.
Other options that shouldn't be used for equilibrium are:
<->
<=>
Software
The current wikipedia software simply doesn't work for chemistry. Until better software is created, chemistry will not be worth adding to wikipedia. Bensaccount 20:38, 6 Mar 2004 (UTC)
I hope you're being sarcastic. For years, chemical knowledge has been distributed using an outdated technology that has no chemistry-specific functions, and science carried on fine. We should decide on what a good chemical diagram should look like, but I don't think there are any issues with putting chemistry on here.
Yes, I have changed my mind. A lot of chemistry can be explained using IUPAC nomenclature. Bensaccount 18:05, 9 Mar 2004 (UTC)
IUPAC nomenclature doesn't explain anything, it is a set of rules as to how you name things. Many common chemicals are known more often by their common names rather than IUPAC. Diagrams are fine the way they are, but would be better if we standardised them. Iridium77 22:02, 9 Mar 2004 (UTC)
IUPAC nomenclature allows you to explain the structure of a compound without a diagram. Common nomenclature is outdated. Bensaccount 03:49, 6 Apr 2004 (UTC)
Which is fine, if you are a computer, and no errors were made in communicating the systematic name. The persistance of common names for many of the most industrially important compounds, however, indicates that for all but the most trivial cases, we as humans are better at memorizing non-systematic names than interpreting systematic ones. Shimmin 04:18, 6 Apr 2004 (UTC)
Ben, to be blunt, it's evident that you're no chemist. The fact of the matter is this: IUPAC is fine for small, simple things. But when you get onto the nasties like, for example, Unadecacyclo[9.9.0.01,5.02,12.02,18.03,7.06,10.08,12.011,15.013,17.016,20]eicosane, you'll understand why it is referred to using its common name, Pagodane. Or more frequently, with a diagram. Or less obscurely, Tricyclo[3.3.1.13,7]decane, a common substituent, and unanimously known as adamantane.
No I am not an exalted chemist like yourself. I am merely a biochemistry student. My comment is not as unheard of as you make it seem. I agree that the diagram makes things much easier for the viewer. I was discouraged because ChemSketch takes so much more effort than drawing by hand. Especially since I had not used chemsketch or uploaded anything before (copying every compound to paint and then saving and uploading and adding to the page...).
Your comment "Common nomenclature is outdated" is frankly wrong. It's certainly not unheard of, we hear it all the time from people who have just come into contact with chemistry.
A little learning is a dangerous thing, drink deep or taste not the pierian spring: there shallow draughts intoxicate the brain, and drinking largely sobers us again
Yes, drawing things by hand is a lot quicker, but it's not so helpful for getting stuff on wikipedia. My point is that you've got to use the right tool for the job. For common molecules, functional groups etc, then the common name is usually the way to go. For moderately complex things, IUPAC may be ok sometimes (2,3 dimethylsalicylic acid is easy enough), for anything more complicated, a diagram is probably necessary.
Given the vast number of chemical compounds I think it would be a good idea to create some kind of standard tutorial for how to create chemical diagrams and how to export them to wikipedia. Either that or have everyone just use IUPAC.
Also, I want to copy a visualization of a protein made with VMD here. Is there a standard program for visualizations, and how do copyrights work on them? Bensaccount22:30, 3 May 2004 (UTC)
Regarding a standard format, I agree. It would be helpful if we could come up with standard settings for the common software (chemdraw, isis, chemsketch) that would make things look smart.
There has been a long discussion on the mailing list about the use of SMILES[1] notation for creating chemistry diagrams. SMILES notation is compact, well-documented, there are multiple tools for it, both Free/Open Source and proprietary. However, it needs the political and programming will for someone to add an extension to MediaWiki that will integrate these tools so we can write (for example) [[SMILES:c1ccccc1[N+](=O)[O-]|right|frame|nitrobenzene]] and get the expected result: a nice automatically generated chemical diagram of nitrobenzene as a PNG, in a frame with a caption. -- The Anome 15:27, 29 Aug 2004 (UTC)
The general exchange format for chemical structures is Molfile. All of the programs (ChemDraw, ISIS and ChemSketch) will read it. ACD/ChemSketch has over 500,000 users. The freeware version supports organic molecules (http://www.acdlabs.com/download/chemsk.html) and allows 3D viewing in an attractive away (http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/3d/). A new version will be released at the end of February and will support polymers and organometallics. To learn how to use it try the movies at http://www.acdlabs.com/download/movies/mov_draw.html (though these are for the commercial version!). The freeware version includes SMILES conversion. To see how molecules can be made to look checkout those shown on Reactive Reports at http://www.reactivereports.com/43/43_1.html. Chemistry NEEDS to be a part of Wikipedia for sure and free software exists to allow it to be visual and entertaining. It is both visual and entertaining month after month at http://www.reactivereports.com/ so why not on Wikipedia? tony27587 15:25, 20 Feb 2005 (UTC)
I've been having thoughts about the balance between providing data and cluttering the page. A minimalist approach to the sidebar would be basic identification info (name, formula/structure, synonyms, CAS), and then external links to an MSDS and the NIST properties database. The next data to include would be the most useful basic properties (formula weight, phase transition temperatures, density). Some articles also feature some thermochemical data, and acid/base dissociation constants if applicable. One could also include stuff like index of refraction, dielectric constant, surface tension, etc...) but at some point, the properties sidebar gets to be longer than the text of the article, and the whole thing seems a bit silly.
I just put a reference to the Chemistry WikiProject on the Chemistry wikipage, which was rather quickly reverted by User:Darrien stating that selfreferencing should be avoided. The proper linking to a WikiProject should be on a Discussion page (see above), but how do we think about putting a wikilink to the project on a wikipage? Wim van Dorst 19:23, 2005 Apr 10 (UTC)
Do want a since colour/layout for the three project templates, perhaps also applicable to the colour/layouts of the chemical infoboxes and other things for the Chemistry projects. Wim van Dorst 20:33, 2005 Apr 12 (UTC).
To let you know: I aligned all three templates that are related to the Chemistry wikiproject.. Wim van Dorst 20:18, 2005 Apr 16 (UTC).
I'm glad to see you're joining the CoffeeRoll standard. However, would you please consider making the image a bit smaller vertically, and making its background transparent (would require changing it from JPEG to GIF) so that it's brown rather than white? Yours, Radiant_* 14:02, May 20, 2005 (UTC)
Good ideas: I couldn't reduce the height without making the picture totally unclear, but I did the transparant idea, and I reduced the picture size as well for faster downloads. Wim van Dorst 22:14, 2005 May 20 (UTC).
I'd like to propose the use of Image:Glasswareb.png for this template. Alpha blending is sorted out in all modern browsers, and looks much better than the hard-edges of transparent blending (ala GIF89). The resulting difference can be seen at [2]
Rocks and Minerals table proposal
I've created a WikiProject Rocks and Minerals for anyone who'd like to join and comment. Tried to use compound table as a start but I think there are differences in the kinds of appropriate info. Comments welcome. Elf 21:29, 4 Feb 2004 (UTC)
I hope to standardize the templates and tables by May 7, 2005. Anyone willing to work on this with me, even for a short time is greatly appreciated. It's the difference between getting this done in five months instead of three years. oo64eva (AJ) 15:28, Apr 5, 2005 (UTC)
Chem-stub template
I upgraded the chem-stub template to a layout similar to the other Chemistry templates. Cacycle, you added a 1em left-margin. Could you please explain (for my education) why? Wim van Dorst 21:37, 2005 Apr 15 (UTC).
The "<br style="clear: both;">" is against overlapping of the template and images in the articles. The 1em is the top-margin, not the left-margin (the order is: top, right, bottom, left), and is needed to separate the article texts and the template. Cacycle 22:16, 15 Apr 2005 (UTC)
Hi, just a little note here... I don't want to get into an edit war, but you'll need to replace the div tag back on the stub. I fully understand you wanting to make it comply with your project's templates, but it must comply with the stub template format to identify it as a stub. Specifically, I am asking that the div tag to be replaced back on to the template. (div class="boilerplate metadata" id="stub") -- AllyUnion(talk) 17:18, 16 Apr 2005 (UTC)
Thanks for pointing this out. I did seek info about what format a template should comply with, but didn't find much. Apparently I should have looked further. Obviously, the div info is back in. Wim van Dorst 19:55, 2005 Apr 16 (UTC).
By way of explanation, and in response to a comment on my talk page: I didn't realize I was reverting it; I did the editing by hand, and intended that the template look like every single other stub template. Avoidable colored boxes are ugly, not to mention an unnecessary distraction from the content of the article. Also, I removed a mention of the wikiproject since convention dictates that an editors' project not be linked from the main namespace. — Dan | Talk 20:35, 26 Apr 2005 (UTC)
Thanks for the elucidation. But where can we find those conventions, standards etc for stubs (and other templates)? We aim to make the Chemistry wikiproject related templates uniform. Isn't that appropriate? And as a {{stub}} notification is by definition an editor's link in main namespace, I would think that guidelines for editing would be appropriate? Wim van Dorst 21:43, 2005 Apr 26 (UTC).
![[2]](http://www.ajs.com/~ajs/images/chemcompare.png){kind=link}