User talk:Synpath

Drawings for thiamine

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.

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]

Apologies for not doing the cloud permissions correctly: I've given you access and this should now work for anyone with the link. Mike Turnbull (talk) 11:14, 25 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.

The style guide has guidelines stating "Make the size of the rings and type proportional. The published size of six-membered rings should be approximately ¼ in. (6.35 mm) in diameter; the published size of five-membered rings should be slightly smaller. The type size should be 5–8 points.", which for 1 cm bond lengths is ~13.5-21.5 pt font. The ACS recommended settings for ChemDraw (courtesy link) are for 0.508 cm bond lengths (fixed length = 14.4 pt) and a font size of 10 pt, which is on the upper end of the guideline range of 7-11 pt font.

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]

OK, good idea. Would you like to summarise what we have discussed and propose something on WT:WikiProject Chemistry/Structure drawing workgroup and I'll comment with a ping to a few editors I know who will have views? You could link my Google .png file if that helps. Mike Turnbull (talk) 22:40, 25 November 2022 (UTC)[reply]

And here I am not knowing the group even existed. I've written a short post and will add it soon. Synpath (talk) 23:08, 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.

Pure speculation from going through something like 10 articles in 15 minutes or so, and my rough knowledge of PC history. Synpath (talk) 19:29, 28 November 2022 (UTC)[reply]

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]

AfC notification: Draft:Imine reductase has a new comment

I've left a comment on your Articles for Creation submission, which can be viewed at Draft:Imine reductase. Thanks! Ozzie10aaaa (talk) 15:31, 28 January 2024 (UTC)[reply]

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Hello

It looks like your interests overlap more with Wikipedia:WikiProject Pharmacology, butwould you be willing to lend a hand with a little project? Wikipedia:WikiProject Medicine is trying to get at least one ref into every medicine-related article. The list is getting shorter, but we've still got a bit more than 100 to go, and the Wikipedia:WikiProject Unreferenced articles/Backlog drives/November 2024 ends in just less than a week. If you could add a source to even one or two of them, it would really help us out. Here's how to help:

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.)
That's all!

Also, if you ever need help with medicine-related articles, please feel free to put Wikipedia talk:WikiProject Medicine on your watchlist, and to join the discussion whenever you'd like. Thanks, WhatamIdoing (talk) 00:09, 25 November 2024 (UTC)[reply]

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.

Also, Integrin alphaXbeta2 in the current state should be BLAR'd/"merged" and point to Integrin alpha X where the complex is mentioned. Maybe it can be deleted in favour of WP:REDYES or expanded, not sure on that one. I'll do a little reading there. ― Synpath 01:27, 25 November 2024 (UTC)[reply]

I've merged and redirected Integrin alphaXbeta2 to Macrophage-1 antigen#CR3 and CR4. After some reading CR4 seems to often be discussed alongside CR3 and that's also the case in Wikipedia. It seems appropriate to redirect there. ― Synpath 01:51, 25 November 2024 (UTC)[reply]

Thank you very much! I always appreciate a good merge or WP:BLAR. WhatamIdoing (talk) 02:56, 25 November 2024 (UTC)[reply]

Dark mode usability issues introduced in "Adding class=skin-invert-image to dark drawings for readability in dark mode per https://www.mediawiki.org/wiki/Recommendations_for_night_mode_compatibility_on_Wikimedia_wikis#Apply_filters_to_dark_images_with_transparent_background" edits

I was reading trough the Adderall article and noticed all of the informational diagrams looked wrong in dark mode. The diagrams had white-on-transparent text with a white background underneath. The three diagrams in question are defined in Template:Psychostimulant_addiction, Template:Amphetamine_pharmacokinetics and Template:Amphetamine_pharmacokinetics. You had the same latest edits on all three diagrams, wrapping them in class="skin-invert-image". This seems to have caused the aforementioned usability issues in dark mode. To make the diagrams usable in dark mode, I had to add | image-bg-color = unset to Template:Annotated image 4 and class="skin-invert" around Template:Annotations.

Were your edits automated in some way?

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. ― Synpath 20:40, 7 December 2024 (UTC)[reply]