User talk:Yikrazuul

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Contents 1 Please link images 2 Suosan.png 3 starting over 4 Flavonoide

[edit] Please link images

BotMultichillT 06:21, 8 March 2009 (UTC)

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[edit] Suosan.png

Hi Yikrazuul, Could you please take a look at File:Suosan.png? It shouldn't have the minus charge at the top right because the charges are already located on atoms within the brackets. Thanks. Edgar181 (talk) 21:00, 5 June 2009 (UTC)

Done. By the way: Is Suosan really the sodium salt of N-(((4-Nitrophenyl)amino)carbonyl)-beta-alanine? According to this or this not...Cheers, --Yikrazuul (talk) 21:49, 5 June 2009 (UTC)

Yes, it looks like maybe it should be the parent carboxylic acid. I'll check Chemical Abstracts on Monday. Edgar181 (talk) 23:04, 5 June 2009 (UTC)

SciFinder tells me that Suosan is the sodium salt, CAS number 140-46-5.

See also Int. J. Quant. Chem. (1994) 51, 335-341. Couldn't quite get the info I wanted out of it, but maybe you guys can.

Ben (talk) 23:30, 5 June 2009 (UTC)

Thx a lot, I'll check that asap. Cheers, --Yikrazuul (talk) 09:47, 6 June 2009 (UTC)

PS: @Ben: Nope. In the publication there is no sodium nor Na in the text. They also write: terminal COOH-group. At least it is mentioned, that Suosan is 700 times sweeter than sucrose. Cheers, --Yikrazuul (talk) 15:08, 7 June 2009 (UTC). PPS: Look also this orthat: no sodium! --Yikrazuul (talk) 15:14, 7 June 2009 (UTC)

SciFinder has 17 references to the sodium salt and 8 to the parent acid. The parent acid has CAS no. 102-66-9.

I've made the results into PDFs:

• Sodium salt, 140-46-5: http://www.benjamin-mills.com/Wikipedia/140-46-5.pdf

• Parent acid, 102-66-9: http://www.benjamin-mills.com/Wikipedia/102-66-9.pdf

Ben (talk) 17:14, 7 June 2009 (UTC)

Thx Ben. Does that mean SciFinder overrules three papers? --Yikrazuul (talk) 18:18, 7 June 2009 (UTC)

No, not at all. I just thought it would be useful to have a list of all relevant papers to give a balanced view of the literature, rather than cherry-picking.

Ben (talk) 16:09, 8 June 2009 (UTC)

Hmm. One odd problem is, that clearly a "parent acid" paper is among the "sodium-salt" papers (answer 9, page 3). On the German Wiki, we have listed both the parent acid and the sodium salt. But impo opinion it seems like that the parent acid IS Suosan. Maybe we should discuss that there? Cheers, --Yikrazuul (talk) 18:25, 8 June 2009 (UTC)

[edit] starting over

Yikrazuul, I'm hoping we can start over a bit here. I've been scanning through your edits here and on WP, and I think we're on the same team here. We're both interested in making things better for science-related articles. I understand you think the Gene Wiki effort is not achieving this goal, but the intent is certainly there. And our effort would certainly benefit from your input and expertise moving forward. On the issue of the images in particular, I'm open to the will of the community here, including everything up to and including deletion of all the images we've uploaded. I just think we need a bit more discussion before we act, just so we get it right this time. I hope we can agree on this common ground. Cheers, AndrewGNF (talk) 17:36, 3 August 2009 (UTC)

Hey Andrew,

I appriciate your contributions here on WP as well, and I'm glad that we can discuss about certain issues. Impo I wouldn't delete those images (as a matter of fact I also mentioned that in that discussion), since - as an IP stated - we are not lacking in webspace here. My point is just as simple as beneficial for the community: In that complicated field of biosciences we should not fully rely on BOT-made entries. BOTs are good for hard- and unpricise work (adding physical data, formating, adding available pdb-links) etc. But the real-work, this "peer-review", humans like we are have to do. Hence I was alerted, I feared that the BOT is uploading virtually every thumbnail of a published structure or part of a structure (compare example):

shorted expample

Phage T4 lysozyme

Phage T4 lysozyme

Phage T4 lysozyme

guess what

I am used to do things on demand: If someone needs a picture he is claiming that. And others like me are doing our best to fulfil their wishes.

Hence I think we will come to an agreement, since feedbacks are - throughout history - always beneficial! Cheers, --Yikrazuul (talk) 18:25, 3 August 2009 (UTC)

Yes, I am 100% agreed that human work should trump bot work every time. We've taken great pains with the Gene Wiki bot to allow users to turn off bot updates for specific pages, and also to avoid overwriting likely human edits even if the flag hasn't been explicitly set. And this principle is even more obvious when looking at the molecular structures. Clearly, doing things individually (and in the hands of domain experts) results in figures that convey much more information by tailoring the coloring, zoom, orientation, etc etc.

It may be a bit naive, but we are hoping that including more thumbnails in the Gene Wiki will lead to a greater appreciation of structural biology and the importance of 3D structure, and then an increase in requests for improved images from visualization specialists like yourself. Ultimately, we're hoping for an eventual net increase in the quantity and quality of visualizations with the Gene Wiki.

With the specific lysozyme example above, I agree that the difference between those four structures is not immediately apparent, especially from the static images hosted here at WikiCommons. I can see a few ways how this could have been handled. We could import all images (like we've done so far) just to have them accessible by any valid PDB ID. We could somehow determine that these are redundant and only load one of them. Or we could skip them all since they deal with lysozyme, and hence won't be used in the Gene Wiki. Any thoughts on the "right" way this should be handled? I'm asking from the perspective of adjusting our past contributions if others feel it important enough, as well as for future contributions if another bot run is approved later. Cheers, AndrewGNF (talk) 20:38, 3 August 2009 (UTC)

Just a short comment: Is it possible to avoid uploading these images in JPG file type? Such images quite often show compression artefacts. The file types of choice are SVG and PNG. --Leyo 06:21, 4 August 2009 (UTC)

Hi Leyo, yes, moving forward we intend to stick with PNG. The problem was that the image server provided by the EBI changed format half-way through our process. Thankfully, they changed the "right" way (to PNG, rather than to JPG). Whether we should replace the existing JPG to the PNG versions is certainly a point of discussion. (BTW, I didn't mean to create a fork of the main discussion at the village pump. Let's move any follow-up and/or other issues back over there? Thanks...) Cheers, AndrewGNF (talk) 15:46, 4 August 2009 (UTC)

We could circumvent one problem (see above) by (1) using a good description. Hereby all relevant data should be pointed out. This could be adressed easily. (2) In addition it should be pointed out (kind of note) those galleries in GeneWiki-articles contain all kind of published structures. They don't show necessarily neither the complete nor the "right" structure.

Hence we could combine (maybe) usefull resources and the objectivity in that regard. Cheers, --Yikrazuul (talk) 19:14, 5 August 2009 (UTC)

I agree, a better description would help a lot. So that everyone can chime in on deciding what's best, I've started a new section back at the village pump. I'm not exactly clear yet on your second suggestion above. Do you propose adding a note to the images themselves, or to the galleries on the Gene Wiki pages? Cheers, AndrewGNF (talk) 00:52, 8 August 2009 (UTC)

[edit] Flavonoide

Hallo Yikrazuul, zwei Fragen zu Flavonoiden:

1. Diese Darstellungsweise mit dem Sauerstoffatom im Ring oben rechts scheint die am weitesten verbreitete zu sein. Bei den Heterocyclen ist es in der Regel aber genau umgekehrt, das Heteroatom weist nach unten: Category:Coumarins. Hast du eine Ahnung, woher das kommt?
2. Laut PubChem sind Oenin und Primulin identisch, nämlich jeweils das Glucosid von Malvidin. Bei dir aber unterscheiden sie sich im Zuckerrest. Hast du eine zuverlässige Quelle, dass Primulin das Galactosid ist? Es wäre ja nicht das erste Mal, dass PubChem falsch liegt... Gruß, --NEUROtiker ^⇌ 12:29, 4 October 2009 (UTC)

Hi Neuro, nun

1. Möglicherweise hat das was mit der Synthese zu tun. Aus Chalkonen werden die ja gemacht. Aber dann müsste man logischerweise fragen, warum das nicht auf den Kopf steht. Vermutlich ist die Nummerierung (O hat die 1 und ist oben) so nachvollziehbarer ;)

2) Witzigerweise widerspricht sich dann PubChem selbst. Oenin bzw. Enin ist das Glucosid, während Primulin als das Galactosid beschrieben wird. Müsste aber noch in ein Flavanoidhandbuch reinschauen, um ganz sicher zu gehen. Gut, dass ich die Dateinamen wohlweislich nach dem tatsälichen Zucker genannt hatte.

Liebe Grüße, --Yikrazuul (talk) 15:58, 4 October 2009 (UTC)

Sehr umsichtig :-). Auch Sigma bezeichnet das Galactosid als Primulin. Nunja, wird sich um eine weitere Ungenauigkeit bei PubChem halten. Wenn du die Möglichkeit hast, in einem Flavonoidhandbuch nachzuschauen wäre das super! Gruß, --NEUROtiker ^⇌ 17:37, 4 October 2009 (UTC)