Hi Synpath. A bit of background. BIOVIA Draw is the current version of the original ISIS/Draw program which I have been using since the mid 1980s, when it was introduced by MDL. Their .mol format files (for individual molecules) are now open-source and widely used, for example by ChemSpider. However their .skc (sketch) file vector graphic format for complete drawings is still proprietary. In its current incarnation, the program can export several image file formats including .png and .emf (the Microsoft enhanced metafile format) but NOT .svg. Hence, to generate Wikimedia-acceptable .svg I use .emf (which Inkscape can read) and make the conversion to .svg in that program.
Thiamine biosynthesis as thumb
MOS:CSDG says we should be using ACS drawing conventions, as you know. These are implemented as a settings option in BIOVIA Draw. Take a look a this .png file in my Google cloud. I can't load this to Wikimedia as it is a screenshot and so copyrighted. If your monitor is set up exactly like mine, the scale bar will be 1 cm on-screen and the drawing (which is part of the thiamine biosynthesis) has exactly the specified ACS settings as shown in the .xml document that the drawing program provides. Note the 10 pt Arial default and the specifications for many other items, not all shown. Now the interesting bit. If I take the corresponding .svg file and include it in a thumbnail, it looks as on the right: however this is not defaulting to 1 cm bond lengths, since the Wikipedia default for thumbnails is 220px total width. To get an image back to the default ACS size of 1 cm bond length on my monitor, I find by trial-and-error that I need to set this particular image to 800px thus:
Since these are the same .svg file, clicking on either will provide a version that is as large as your monitor will allow. I'm going to reset all the drawings in the thiamine article so they appear at the same 1 cm bond length on my monitor, which I hope will satisfy your plea for consistency. Nevertheless, we may get complaints from other readers that the diagrams are too large, depending on individual output devices. Mike Turnbull (talk) 14:51, 24 November 2022 (UTC)[reply]
@Michael D. Turnbull thanks for the screen grab of your Biovia diagrams with the XML settings. I see that the diagram is faithfully reproduced as an svg, and now think that the issue is that the Biovia ACS template does not reflect the current ACS recommendations.
Thanks for putting up my bone crushingly low stakes nonsense. I just see this as an easy quality of life fix for an article looking to upgrade its rating. Synpath (talk) 19:36, 25 November 2022 (UTC)[reply]
Also, side note: thanks for your contributions over at Teahouse and the Science Reference Desk. I've been reading through that on and off the past few weeks and got a feel for what Wikipedia policies and editor culture are from there. Synpath (talk) 19:52, 25 November 2022 (UTC)[reply]
Maybe this is a discussion we need to take wider. I'm not sure when the current Wikipedia MOS:CSDG were first proposed and to what extent they have subsequently been revised. I suspect that the ACS guidelines have changed since they now probably take camera-ready diagrams when previously they redrew what contributors supplied. The other issue is that whatever guidelines we set, WP editors will often ignore them, so the issue is the balance between wanting contributions and wanting standardisation. As an (ex) professional organic chemist working in industry, I think that the majority of WP chemical drawings are pretty good even without stringent adherence to standards. Do you think that we should press for more standardisation and if so, can you give some examples of currently bad practice you would want to change? I'm willing to help do that if, on balance, readers would benefit. Mike Turnbull (talk) 20:42, 25 November 2022 (UTC)[reply]
Essentially the first version of MOS:CHEM(4 Mar 2008) stated the adoption of the ACS style. I'd imagine this implies the most up to date version of the guidelines rather than whatever was written at the time.
Also, I absolutely agree that most articles with chemical diagrams are solid, even though achieving strict adherence to any style guide on Wikipedia is a pipe dream. For example, the diagrams in Aldol reaction vary widely and some don't strictly follow ACS, but they're all clear and easily legible. When I do see issues it's usually on discipline specific (i.e. obscure) start/C-rated articles, as you might expect. For example, the mechanism at Serine Protease has a mostly fine diagram (sloppy arrows and debatable geometry aside), but it suffers legibility issues while scaling down. This diagram could be made more legible by applying the ACS style.
I think there's a reasonable expectation that an article receiving a GA rating or above wouldn't have small quality of life issues like that. If that's not a requirement for GA, then it might warrant discussion. Otherwise, I can see talking about adding a note on Biovia ACS template settings to MOS:CSDG. Synpath (talk) 22:19, 25 November 2022 (UTC)[reply]
Thanks for doing that. I want to do a bit of research regarding Biovia Draw and if possible work out why it appears not to follow the ACS convention when it has a specific template which says it does! That will take a few days and I'll post at the workgroup page when I reach a conclusion. Mike Turnbull (talk) 16:30, 27 November 2022 (UTC)[reply]
I was interested in why that might be too, and I searched through the some of the top cited articles in JACS from 1980-1990 (which I was surprised to find that they are mostly computational chemistry with few complex structures). The quick summary of what I found was that there was not a lot of consistency in how structure diagrams were rendered. Maybe the early 80s looked reminiscent of 70s (manual?) typesetting, but besides that not too many patterns. I wonder if around that time there were no real guidelines/competing guidelines for chemical drawings while academics and journals adapted to PCs with graphics/GUI software.
As I've mentioned on the Project page, it turns out that this whole mess is my own fault. I thought I was using ACS settings but it turns out I had mistakenly altered them on my local computer and saved the wrong configuration in a personal profile. I'll go back now and redo all the diagrams in the thiamine article at the new settings. Thanks very much for prompting me to get to the bottom of this! Mike Turnbull (talk) 14:32, 29 November 2022 (UTC)[reply]
Oh no! I hate it when software doesn't work the way you want/expect it to. (Why is there no 'undo' in Pymol for visual changes!) At least we've figured out the disconnect, and all the best. Synpath (talk) 17:41, 29 November 2022 (UTC)[reply]
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Pick an article from the list. Most of them are organizations, people, or other subjects that do not require any specialized medical knowledge.
Find at least one reliable source and add it to the article.
Remove or update any maintenance tags at the top of the article.
Edit the list to mark off the item or leave some notes about it so the next person will know that this one is done. (Try editing the page in the visual editor, because it's much easier for tables.)
I am much more interested in molecules and proteins, but Quarantine Act 1721 caught my eye since that seemed like it should easily be notable and have several reliable sources available. And it certainly does, I added two based on the similar Quarantine Act 1710 found as a subsection at Quarantine.
I am not sure if your edits, or some upstream changes to included templates made the diagrams unreadable in dark mode. Please double-check that all edits where you added class="skin-invert-image" don't introduce usability issues in dark mode. Thanks, Susko3 (talk) 19:38, 7 December 2024 (UTC)[reply]
I was worried that some of my edits were introducing inconsistent effects for dark mode since adding class=skin-invert-image has no effect on the mobile app. For me and my browser the diagram was perfectly legible in dark mode and the only visible difference between my edit and yours for {{Amphetamine pharmacokinetics}} is that the background is now transparent rather than black in dark mode. I'm unsure of how I would go about testing the visual effect of edits for other browser settings. For reference I'm on Firefox 131.0.2 and will update to the newer version soon-ish. I plan to tinker and ask around, and I welcome suggestions. In the mean time, I've slowed down making these types of edits in case I end up having to undo them all. ― Synpath20:40, 7 December 2024 (UTC)[reply]
He is the main contributor to the Niacin article, and he is opposing the rename. I couldn't really understand his arguments & point of view. Anyway, just letting you know.
Your edits to the dab page ran afoul the dab formatting guidelines/practices and definitely sparked some grumpiness. My edits probably should have waited for the RM to close too, but the RM is old, I thought I had a reasonable alteration and be bold and all that. Maybe its also one of the more polite elbow nudges I can throw out.
The niacin naming issue is just plain confusing, and its even sometimes unclear what compound journal abstracts are referring to. What I found after reading some of those abstracts in niacin was that articles coming from more clinical-oriented research tend to refer to nicotinic acid as niacin, and no other molecule as niacin. Governments and thus regulated food labels use niacin more as a stand in for vitamin B3 varieties. If I had to guess I'd say David notMD is an academic that comes from a clinical research setting and that niacin=nicotinic acid usage is by far the primary topic for them. I can definitely just be wrong in some way and I haven't actually read the entire RM discussion, as that probably has gone on for a few too many bytes in my opinion. ― Synpath03:19, 8 January 2025 (UTC)[reply]
Arthurfragoso, Synpath For background, yes, my PhD and career were in nutritional biochemistry, and I am the person who raised Niacin from B-class to GA in 2020. I do not pretend to 'own' the article, but I do have a strong opinion that Niacin is the better title for the article. David notMD (talk) 12:50, 8 January 2025 (UTC)[reply]
Taurine is an amino acid that doesn't carry a carboxylic acid group, therefore the definition of amino acid is stated as follows: a compound with both acid and amine functional groups.
I am aware it's most commonly defined as a carboxylic acid, but this fallacy is called appeal to the people, in cases of such scientific definitions, being popular doesn't achieve truth.
If by definition an amino acid must have a carboxylic function, then it's either Taurine isn't an amino acid or that is not the definition of an amino acid. MeAbdelkrim (talk) 09:46, 23 May 2025 (UTC)[reply]
I'd be interested to see a reference that pins down the definition of an amino acid to "any organic molecule with an amino group and acidic functional group". I haven't found one. Most provide definitions relative to proteinogenic amino acids, i.e. amino + carboxylic acid. Such a permissive definition has problems as it puts molecules like phosphatidylethanolamine, sphingosine-1-phosphate and phosphorylated glucosamine into the category of 'amino acid'—not a very helpful definition for the study of metabolism and biology.
There are plenty of references online that imply that amino acids don't need a carboxylic acid to be classified as so, for example PubChem classifies Taurine as an amino acid.
You are right in that molecules like phosphatidylethanolamine should be classified as amino acids based on this broad definition, I don't find a reason not to include them as amino acids, they won't lose their belonging to phospholipids by doing this.
I will undo my changes in the amino acid Wikipedia page, but I would like to hear your response on how to approach this problem, formalizing a definition by excluding molecules like Taurine from the amino acids class or having the definition include molecules such as phosphatidylethanolamine, both situations are problematic, perhaps it's worse not having a definition for an "amino acid" as the situation is now. The reason "organic compound containing both a carboxyl (—COOH) and an amino (—NH2) group" is not the definition is because it doesn't align with Taurine being an amino acid. MeAbdelkrim (talk) 15:08, 23 May 2025 (UTC)[reply]
The textbook definitions of amino acid I've seen basically just cite the structure of a generic proteinogenic amino acid and move on from there. That's a suitable, citable definition. When there are exceptions (e.g. alternate acid group), the difference can be described and citation provided supporting it is typically grouped with amino acids despite the difference. It's not as satisfying as a single unified definition, but it is basically how the term is used. ⇌Synpath16:11, 23 May 2025 (UTC)[reply]
I didn't realize this would raise lint errors. I could wrap this in a custom span or something to get around it, but that seems like bad form too. Would you have suggestions? Otherwise, I'll keep looking into it and maybe just revert that particular addition. Relatively few of those boxes have signatures. ⇌Synpath23:53, 1 August 2025 (UTC)[reply]
I swapped the class onto the table's td element and switched up the CSS. I'm not seeing the lint error for the testcases subpage, so I think that fixed it. ⇌Synpath00:18, 2 August 2025 (UTC)[reply]
Hi Synpath. As mentioned in your thread, I've used the template at Acetylserotonin O-methyltransferase#Reactions catalyzed and in doing so some questions/comments arose. Check out {{Chemrxn|width=50%|
{{Chemrxn/sub|[[File:Metoxindolacetato.png|frameless|class=skin-invert-image]]|caption=5-Methoxyindoleacetic acid}}
{{Chemrxn/cpd|5-methoxyindole-3-acetic acid}}
}} which gives
5-Methoxyindoleacetic acid
[[File:No image file is associated with 5-methoxyindole-3-acetic acid via Wikidata. Try a qualifier ID or use chemrxn/subunit.|frameless|class=skin-invert-image|alt=2D representation of the chemical structure of 5-methoxyindole-3-acetic acid.]]
The first "sub" uses the underlying file from Wikidata at 5-methoxyindole-3-acetic acid - Wikidata but trying to use it directly in the second "cpd" line gives that strange output, despite the same "cpd" syntax working perfectly well with 5-Hydroxyindoleacetic acid.
Less important but worth mentioning is that I can't work out how to suppress the Wikilink (i.e. avoid the redlink) although you have provided a |link= parameter to force a target, if needed. Would something like |link=null be useful? Mike Turnbull (talk) 16:48, 9 November 2025 (UTC)[reply]
{{Chemrxn/cpd|5-methoxyindole-3-acetic acid}} returns null output rather than an error after not finding the name "5-methoxyindole-3-acetic acid" in Wikidata. This is odd since the compound does have a page. I can make this clear by outputting an error with {{Error if empty}}, but I'll have to look closer to see why this didn't work in the first place.
Also, I actually made a choice to always force a link since I was wrongly assuming that chemicals with a wikidata item would also have and article/redirect associated with them. I can rework that so that the link needs to be made manually by the editor. No additional mucking about with a link= parameter, just write whatever wikitext you want for the caption. So input for 5-hydroxyindolacetic acid could look like: {{Chemrxn/sub|[[File:5-Hydroxyindolessigsäure (5-HIAA).svg|frameless|class=skin-invert-image]]|caption=[[5-hydroxyindolacetic acid|{{nowrap|(5-Hydroxy-1H-indol-3-yl)acetic}} acid]]}}.
Wikidata has an enormous number of compounds which don't have en: articles, since a lot were cross-loaded from PubChem or ChemSpider (I forget which). Many won't have images, although some that are missing articles in English will have them from e.g. German, French or Spanish articles: hence the "Metoxindolacetato.png" in the case discussed here. Your idea of having an error message if there's no image in Wikidata is a good one. Editors who run into that message can either look for an existing image on Commons that could be added to the Wikidata record or upload an .svg to Commons and make Wikidata link to it. A later piece of work is going to be to document all this in your template pages! Using nolink sounds good. Mike Turnbull (talk) 12:17, 10 November 2025 (UTC)[reply]
The template being transcluded is the same (i.e. {{Chemical reaction}} has {{Chemrxn}} as a shortcut). However, I think you need shortcuts for all possible combinations, or when editors mix things up the result will be as above. The same problem does not arise with {{Chemical reaction|width=80%|
{{Chemical reaction/cpd|Citrulline}} }} which gives
You could, of course, insist on expanded parameters like "compound" everywhere, which might make the syntax clearer to non-specialists who looked at the source code. Mike Turnbull (talk) 17:09, 9 November 2025 (UTC)[reply]
A good point, I'll make the redirects. Explicit parameters for compounds at the level of the wrapping template TM:Chemrxn would work, but the template source code will quickly get verbose. It's a bit of a style thing and I think the current implementation is one of the simpler ways of implementing the template. Though it comes at the cost of a weird way of inputting values as nested consecutive templates instead of distinct parameters. ⇌Synpath22:51, 9 November 2025 (UTC)[reply]
Yes, I wondered why the implementation required multiple template calls but I quickly got used to it. One template call per reaction subcomponent is actually quite intuitive and, I suspect, more versatile in the long term. Mike Turnbull (talk) 12:19, 10 November 2025 (UTC)[reply]
I've just edited the Thiopurine methyltransferase article to add a typical reaction. I had to draw the product and add it to Wikidata but that part went well. (As an aside, this seems to be another case where the image isn't picked up using the |cpd method). However, I found a strange interaction between the width parameter and the upright one. My problem was that the the image for the starting material was slightly smaller than the product when I took a width of 45%, namely {{Chemrxn|width=45%|
{{Chemrxn/cpd|Mercaptopurine}}
{{Chemrxn/txt|+ [[S-Adenosyl methionine|SAM]]}}
{{Chemrxn/arw|direction=forward}}
{{Chemrxn/sub|[[File:6-Methylmercaptopurine.svg|frameless|class=skin-invert-image]]|caption=6-Methylmercaptopurine}}
{{Chemrxn/txt|+ [[S-Adenosyl-L-homocysteine|SAH]]}}
}} giving
No matter how I fiddled by adding |upright= to one or other of the images I could not get them to be the same size. Then I tried altering the width parameter and to my surprise found that it changed the size of the starting material but not the product and with a value of 55% I got exactly what I needed! Clearly, something odd is going on. Mike Turnbull (talk) 15:45, 10 November 2025 (UTC)[reply]
This is a bit of a unintuitive interaction I didn't consider. For most cases of a reaction scheme, the minimum size of the image is determined by the longest word in the caption. This can get pretty long for chemical names, and so some images may get stuck looking very large. In those cases, upright can only make images smaller than that minimum length and not larger. See:
upright=1.7 -- Note: the effect becomes obvious only for smaller template widths. If all the images look identical slowly decrease the width of your browser window and see how they scale.
WWWWW
WWWWWWW
WWWWWWWWW
WWWWWWWWWWW
WWWWWWWWWWWWW
upright=0.7
WWWWW
WWWWWWW
WWWWWWWWW
WWWWWWWWWWW
WWWWWWWWWWWWW
upright=0.3
WWWWW
WWWWWWW
WWWWWWWWW
WWWWWWWWWWW
WWWWWWWWWWWWW
However, when there is excess horizontal space in the scheme uprightcan make an image larger than the caption, see (again this demonstration is dependent on your browser window size):
I'm glad you know what you are doing as this would certainly have foxed me! I don't think you need a "perfect" answer as anyone who becomes familiar with the template will soon learn the sort of tricks that help sizing tweaks, including the possibility of using upright < 1 on one component and > 1 on another. The main issue, I think, is not to have the width parameter interfere with the upright one. Width should, IMO, just scale the whole diagram into a final size, although I appreciate that may be difficult as you need the text font to be constant as seen by the reader. Meanwhile, I'm continuing to use the template in live articles as "what links here" on the template page will show. This is giving me some ideas, one of which I'll mention in the next section here. Mike Turnbull (talk) 11:51, 11 November 2025 (UTC)[reply]
Unfortunately, I don't think I can currently get the CSS to behave in a way where upright will always determine the relative size of the images before everything gets scaled to the template width. The change I made yesterday is surprisingly the most durable solution after doing some more testing today, and I think it lets upright be usable though it might require some trial and error. All I could do to improve it was adjust the captions to not overlap. I'll have to read up on how html image elements interact with flex flow to make more progress on this. ⇌Synpath02:55, 12 November 2025 (UTC)[reply]
@Michael D. Turnbull: I've finally updated the live template from the tweaks I was making in the sandbox, then updated some of the transclusions you made over the past couple of days. The template is much more reliable in how it displays now, and (dare I say) it felt pretty good to use. It still needs polishing imo. But, my goodness, thank you so much for testing this out with me! It would have taken me so much longer to even find these display and usability issues. ⇌Synpath02:54, 13 November 2025 (UTC)[reply]
This idea addresses two current issues. The first is that some compounds are giving error messages despite being on Wikidata. 6-Methylmercaptopurine is an example. The second is that some chemical names are very long and prone to typos when entered by an editor who wants to use the "cpd" method of lookup. This is less of an issue with the "sub" method, as filenames tend to be more user-friendly. My suggestion is that all three of
[[File:No image file is associated with 6-Methylmercaptopurine via Wikidata. Try a qualifier ID or use chemrxn/subunit.|frameless|class=skin-invert-image|alt=2D representation of the chemical structure of 6-Methylmercaptopurine.]]
should work. The middle uses "sub" and the first uses "cpd" but fails for an as-yet unknown reason. The third is a new proposal: make "cpd" accept Wikidata Q-numbers directly as an alternative to typing a long name (or, indeed, any name). Thoughts? Mike Turnbull (talk) 12:12, 11 November 2025 (UTC)[reply]
After another day using the template successfully, I note that {{Chemical structure|qid=Q27103606|caption=6-Methylmercaptopurine}} already gives
Yes! I knew I forgot something with that one - I can quickly put it in. Also, I am now suspecting that the compounds that are being missed on Wikidata despite having an entry are those that start with a number. This might be a syntax issue. ⇌Synpath02:59, 12 November 2025 (UTC)[reply]
For example:
[[File:Error: No Wikidata entry found.|thumb|class=skin-invert-image|5-beta-dihydrotestosterone|alt=2D representation of the chemical structure of 5-beta-dihydrotestosterone.]]
Guessed too soon. The issue is that Wikidata info retrieval template only works when Wikipedia article names or Q-IDs. Names associated with the Q-ID of a Wikidata item are not enough. That makes a lot of sense. Examples:
Perhaps the best case would be to output a more informative error message after failing to find a Wikidata item by name. Something like: "No Wikidata entry is associated with ARTICLE NAME. Try a qualifier ID." ⇌Synpath04:37, 12 November 2025 (UTC)[reply]
That's interesting and somewhat unexpected. Not a serious issue now the qid is working. Your error message could say "try a qid or filename" or similar, since both are now alternatives. The filenames need to use Chemrxn/sub not Chemrxn/cpd but editors familiar with the template would know that. Overall, I think that it is shaping up very well. Incidentally, I don't support someone's suggestion of making the arrows longer as the total width of a diagram is always the biggest constraint. However, I'd support making the arrowheads clearer: see File:Thiamazole synthesis route B.svg for one of my drawings which uses the standard ACS settings as specified at MOS:CSDG. Mike Turnbull (talk) 11:07, 13 November 2025 (UTC)[reply]
I'm now getting much faster at this, with the qid parameter being a real game-changer since all I really need to do is draw the individual components that are missing, upload them to Commons and make the Wikidata link. I've now reviewed all the articles in {{One carbon transferases}} and either done them or decided they were already OK. Mike Turnbull (talk) 13:12, 13 November 2025 (UTC)[reply]
I agree on updating the arrow legibility with an all-round 'bolder' version. It's just that it would require something like 32 images of arrows (48 if you also want the reverse-only direction). Before doing that, I would want to see if I could do some image stacking trick to bring it down to 6-7 images. This would a neat case to draw a simple svg on the fly.
I'll update the error message as well
I'm so glad you're finding the template has good use cases—I had thought there was a good chance the general response would be to just make the svg schemes. ⇌Synpath01:56, 14 November 2025 (UTC)[reply]
Hey, these are great! I think that even the most pedantic chemistry nerd would approve your new set of arrows. To be fully useful in standard chemical reactions, there needs to be a way to place text in the same font as the captions to the compounds above (and maybe below) the arrow. So isopropanol to acetone would have something like NaBH4 using {{chem2}} and acetone to isopropanol might have CrO3. You don't need to go overboard on the text allowed as WP:NOTTEXTBOOK applies to these schemes. About the level in my earlier example at File:Thiamazole synthesis route B.svg would be perfect. Mike Turnbull (talk) 11:34, 25 November 2025 (UTC)[reply]
I approve of the way you've done the examples in the main sandbox_templates. Now I look at them again, I think that the arrows are too bolded, as you suggested. This is not a big deal but their width should probably be more in line with the bond widths of the chemicals at that scale. More importantly, you have used a parameter |width= for what I think should definitely be renamed |length=! I guess that you were thinking in terms of the overall width of the image, as for the chemrxn parameter of the same name but using that name for both would be confusing, I think, and an arrow's length is more obvious nomenclature. I especially like the auto-wrapping of the text to fit the arrow. Mike Turnbull (talk) 12:06, 26 November 2025 (UTC)[reply]
Hi Synpath! I patrol CAT:MISSFILE, and was noticing that one of your edits to {{Chemical reaction/arrow/testcases}} added a non-existent file to the template yesterday (the first reaction arrow under the "Resonance" section). I would fix it myself, but I'm not super experienced in template editing and don't want to mess up any of your work. When you get a chance, could you take a look at your edits again to correct the missing image error? Thanks so much, KatnissMay the odds be ever in your favor ♥14:31, 17 November 2025 (UTC)[reply]
I'm adding some functionality to the TM:Chemrxn/arw template that it didn't have before and testing it in the background. The live template can't digest the input and tries to find a file that doesn't exist. The new arrow isn't quite ready to go live, but I can modify the testcase since it isn't useful testing functionality that I know doesn't exist. Thanks for your vigilance! ⇌Synpath15:08, 17 November 2025 (UTC)[reply]
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Hi Synpath. I'm making good progress on List of EC numbers (EC 1) and the template is working well. I've run across a couple of minor issues. At L-iditol 2-dehydrogenase I initially forgot the |frameless|class=skin-invert-image for one of the files I used but when adding it and actually trying dark mode using the binoculars icon provided next to usernames on my standard PC + browser I found that this image is still blacked out while the chemrxn/cpd image was fine (i.e. became white on black). Is this a bug? I'm not even sure that the frameless parameter is now required. See that article's history for my edits: currently there is a filename but no extra parameters.
When adding reaction diagrams I now often add the template {{KEGG enzyme}} as a reference. Its not one of yours but can you explain why it gives a small font and maybe fix that if it wasn't deliberate? Compare this reference[1] with this.[2]
That's exactly why it appears small in the footnotes. It seems that the template is often used in the body of the article (e.g. Fructose 1,6-bisphosphate) and there the font size looks more sensible. Though, in the linked page and similar examples, that way of linking to KEGG is very confusing. The KEGG identifiers are spatially separated from what they refer to. These should be co-located as footnotes, for intuitive clarity, as you are doing. {{KEGG enzyme}} is transcluded about 70 times so it's tractable to manually fix these uses, then remove the span tags. I would volunteer to do so, as well. This assumes that there isn't a different use I am not seeing. Maybe <ref> or {{efn}} could be built into the external link template to make it clear that this is how it should be used. Documentation would also help. ⇌Synpath21:31, 23 November 2025 (UTC)[reply]
Agreed. The example you gave for Fructose 1,6-bisphosphate is not exactly intuitive and I see no harm if it were at standard font size, since the compound and enzyme links currently don't match up with the material they are describing anyway. The way I use the template will come to dominate long-term, I think. It is already about 50 of the 70! As you say, it is just the documentation that needs to change, not the actual template, other than to fix the font size. Mike Turnbull (talk) 11:39, 24 November 2025 (UTC)[reply]
Sorry I couldn't respond earlier.
For L-iditol 2-dehydrogenase your initial fix would have worked, it just didn't get wrapped in the double brackets of the file link. And you're right, frameless isn't required, but the upright parameter only works when used in conjunction with frameless. For example, I made this change at L-iditol 2-dehydrogenase to demonstrate. Would it be nice to have an option for TM:Chemical reaction/subunit that accepted an image file name and added the file linking automatically?
This has me thinking I should default the template to use the skin-invert-image class for images. This won't require any AWB runs to change existing transclusions since duplicates of this CSS class shouldn't change the behaviour of the CSS rules. Though, I can imagine that there might be a situation where one would want to opt out of using skin-invert-image, so I'll make a parameter to opt out. It'll be called something cumbersome like noskininvert. ⇌Synpath21:18, 23 November 2025 (UTC)[reply]
Thanks for the explanations. Now I'll put the skin-invert-image in the correct place! The interaction between frameless and upright would never have occurred to me but makes sense now you mention it. I'll defer to you for how you implement all this in future: just keep the documentation in step with your changes! Mike Turnbull (talk) 11:43, 24 November 2025 (UTC)[reply]
I think I'm keeping on top of the documentation, but its minimal and split up into the subpages as well. I'll need to centralize it and elaborate a bit more on usage. ⇌Synpath01:33, 25 November 2025 (UTC)[reply]
Thank you very much! I always appreciate a good merge or WP:BLAR. WhatamIdoing (talk) 02:56, 25 November 2024 (UTC)
Done ⇌ Synpath 23:43, 23 November 2025 (UTC)