Wikipedia talk:WikiProject Chemistry/Structure drawing workgroup/Archive Jul 2007

Repository of ChemDraw (etc) image originals

Is there any facility within Wikipedia to store the original chemical structure drawings (e.g., .cdx ChemDraw files) used to generate the image files (e.g., .png)? For example, I'd rather not have to redraw the whole Image:Enolate aldol mechanism.png just to fix a missing negative sign and some minor typographic formatting. DMacks 20:04, 6 June 2007 (UTC)[reply]

This is an interesting idea, but I don't know if we have the technology to do it. With one ozonolysis image I did a crude fix in Irfan View recently, because there was a mistake in the image; I would have loved to have had access to the original (the person posting it was no longer active). Does anybody know how we can share/archive these files? BTW, I was confess to being the person who missed the minus sign - I DO have the original ChemDraw, so I'll try & get it fixed tomorrow. Sorry! Walkerma 06:52, 7 June 2007 (UTC)[reply]

PS: Let me know what typographical changes you are proposing, I can do those too. Walkerma 06:54, 7 June 2007 (UTC)[reply]

Specific image issues:

Is there variation among the captions for individual molecules in the image? "enolate" (row 1 structure 2) and some others look bold but others look non-bold, and inconsistent capitalization. Very minor issues obviously, but if one had the ChemDraw and were fixing other stuff anyway, may as well check.
I was pondering nuking the titles ("base-catalyzed aldol reaction", etc.) entirely, per guidelines. Better to leave that kind of thing in the wiki page itself instead of embedded in the image. If an image really does have two distinct parts and needs two different titles in the middle, maybe that's a sign that the image should be split into two images, each for its specific reaction conditions and with a (wiki-page text) description. Again, this could all be done using GIMP or PhotoShop, but while we're ChemDrawing...

I just noticed that ChemDraw can save images in "ChemDraw XML" format (.cdxml), which is plain-text and therefore could be stored on the image page. Would require cut'n'pasting via a text editor to transfer the file, so not ideal. Or we could go old-skool and binhex the .cdx:) DMacks 07:13, 7 June 2007 (UTC)[reply]

Well, the idea sounds interesting. Uploading proprietary file formats kind of goes against the Wikipedia philosophy, though. What you propose is quite doable if we upload SVGs instead of PNGs, which are the object and the code at the same time. Then one would be able to make changes to uploaded files using an editor like, e.g., Inkscape, or even a text editor like Vim. This is admittedly not as good as having access to the original chemical drawing program source, but nearly so. Including the "source" in the image page is an option, but I'd strongly oppose to uploading a file format that requires non-free software to manipulate. I'd rather have nothing than that (but that's just me, of course). I sketch the skeletal formulae with ChemTool, which is free software. I'd gladly upload the ChemTool code (which is quite concise) for each of my images, except not many people seem to use ChemTool. Or should I, anyway? — isilanes (talk|contribs) 19:00, 7 June 2007 (UTC)[reply]
- Well, these software are de-facto industry standards and you'd find most professionals using them. I see a great value in having the original file to edit. Wikipedia currently has problems with SVG files containing text so I wonder how useful that will be. Also, INkscape should not be used to edit these images because manually drawing a bond instead of letting the software do it will look "off" compared with that generated by the software. I do accept that there may be some extremely talented people who can draw chemical structures using inkscape but I think that is the exception, not the rule. --Rifleman 82 02:43, 8 June 2007 (UTC)[reply]
  - I cringe at the use of expressions like de-facto industry standards, specially in IT. By the same rule, Windoze is the de-facto standard for OSs, JPEG and GIF (not PNG or SVG) for images, MP3 and WAV (not Vorbis) for audio, WMV (not MPEG or Theora) for video, the Britannica (and not Wikipedia) for encyclopedias... I wonder what I am doing supporting free knowledge and free software. After all, they are not "industry standards". About SVGs requiring an artist to modify... it depends on what kind of modifications you want to make. If the modification consists on removing excess items, it is trivial. If it consists on moving some item around, it is trivial. If it consists on manipulating text, it is trivial. I have even shortened/enlarged bonds (with a text editor!), simply by changing the (x,y) of one end of the line that defines the bond. More complex changes... yes, they might be difficult. For that, I'll upload the ChemTool source too. — isilanes (talk|contribs) 09:25, 8 June 2007 (UTC)[reply]
    - Fine and well, your comments about "industry standards". But, how many here contribute by linux, let alone use chemtool? Compared with how many chemists use chemdraw, isisdraw, chemsketch, etc? I'm all for free and open standards and software but there are some realities here, and I don't see Wikipedia as the platform for evangelism. --Rifleman 82 15:56, 8 June 2007 (UTC)[reply]
    - For chemical structure drawings, the image file is a secondary or derived format from some native "chemistry" format, and chemists are generally most familiar with chemistry drawing programs. Having the original format available (whatever format that might be) is pretty useful in the general case (i.e., regardless of how severe an edit is needed). I agree with Rifleman here, and think Wikipedia should be about lowering the bar for contributing. Perhaps I wasn't clear when I began: I don't care what format we use~~(and would almost prefer against .cdx precisely because it is not very portable)~~. There are enough formats and converters (hello, OpenBabel) that there oughta be something that is widely "usable" even if not native for all. DMacks 16:24, 8 June 2007 (UTC)[reply]
  - OK, I've reformatted the aldol images (incl. the enol ones). Thanks for the feedback. Let me know if there is anything further you would change. Regarding bold/not bold, etc, that must be something in the image processing or the browser. The ChemDraw files used standard ACS settings as per the style guide; the only deviation was the use of the symbol font for the minus signs so you can see them. Walkerma 05:14, 8 June 2007 (UTC)[reply]
    - Looks good (modulo what I guess is some local display issue). Thanks for the fix and double-checking. DMacks 06:06, 8 June 2007 (UTC)[reply]
SVG looks really interesting to me (code and not a file and therefore interchangeble). Chemtool is not for Windows therefore limited utility. I played around with BKchem also free software http://bkchem.zirael.org/. for example:

but there are some issues with subscripts so for now I will not recommend it. V8rik 19:59, 8 June 2007 (UTC)[reply]