User talk:Cacycle/Archive 01

This is the archived content from my talk page.

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Sayeth

Hey Cacycle! I just wanted to complement you on some great work on Wikipedia. The pharmacology pages have been needing some attention for some time and you apparently know what you're talking about. Sayeth 22:08, Aug 18, 2004 (UTC)

Indole

Hey Cacycle, thanks for your rewrite of indole. Great work! Keep up the good work -- Wikipedia really needs you. Regards & happy editing, Wile E. Heresiarch 14:54, 23 Oct 2004 (UTC)

Chemical Structures

I noticed you added many nifty chemical structure diagrams. Do you use simply an image editing program (Photoshop, etc.) or do you have a specific chemical structure sketching program that you use? I've been looking for a decent one for awhile, and haven't found one... perhaps you could direct me to whatever you use? Thanks, ugen64 23:35, 3 Nov 2004 (UTC)

I've been using ChemDraw and Photoshop, but that's overkill. The trick is to increase the size to 300% or so, to export as an image, and to sample the image size down again, at least as long as the molecule editor does not give acceptable results alone. See also molecule editors and Mykhal's page for his technique.

Thank you so much for your contributions- there are so few chemists on Wikipedia, your contributions are sorely needed, things like the mechanism for the Fischer Indole Synthesis. I was delighted to see benzofuran on there- even if just simple info- as I spent three years making studying benzofuran derivatives! The ChemDraw files are great (though I use IsisDraw myself, but that's just a leftover from when ChemDraw wasn't available on Windows). I do have one picky little point, though. Please could you draw your lone pairs as dots, rather than as lines? It's my understanding that the line representation is considered obsolete (though admittedly it's a lot easier to draw!).

Could we recruit you to become a participant on Wikipedia:WikiProject_Chemicals?

Thanks again, and keep up the good work,

Walkerma 15:50, 18 Jan 2005 (UTC)

Strychnine structure

Hello, Mr. Cacycle. You have overwritten Image:Strychnine.png with your own version, which is unfortunately wrong. Could you tell me where did you find this structure? I have spent not little time on this. My version is in accordance with Beilstein Crossfire, Scifinder, Chem ACX, ... but most important "proof" of the structure is X-ray, as included in Cambridge Structure Database. I have used it to include stereo configuration on all chiral atoms. Please do not waste me work without asking. Thanks, Mykhal 01:12, 4 Nov 2004 (UTC)

Hi Mykhal - I'm sory that I have accidentally changed your strychnine image with a remake of my old and wrong structure. I didn't realize that we have two different strychnine images. I also missed your comment about the wrong double bond. I have corrected the structure and I have changed the strychnine illustration. I'm still a bit confused by the way this system works (and often not works), I think I have even accidently reset the change I made to your upload?!

You should read something about images, or just try to track and see how it works. If you try to upload the image which is already present, the system will warn you about it. If you agree anyway, the old image still remains in history. But you have deleted my images from history! I wonder if you are admin.. Mykhal 20:54, 4 Nov 2004 (UTC)

Anyway, I have just seen your molecule contributions and really like the way you do it :-) BTW, is there a reason that you use transparent backgrounds? Cacycle 15:36, 4 Nov 2004 (UTC)

I think structure formulas should be transparent the same way how font letters are.. To have the same background like the rest of the page. Mykhal 20:58, 4 Nov 2004 (UTC)

SMILES strings

Do you think that SMILES strings are of such importance that they should be included in infobox? Personally I would put them somewhere near the end of the article, rendered with <small> font.

You are right, they might be placed a bit too prominent, especially the longer ones. I put them there too keep chemical data in one place. The SMILES string is thematically related to the chemical name and the structure image, even if most readers are probably not that much interested in it, but that's probably also true for most of the other chemical data.

Mhm, the Image page could be an alternative place, but then nobody would find them. I know a discussion forum that has a SMILES markup and you can decide if you want the SMILES structure displayed by an applet or as plain text. A mechanism displaying the SMILES string after clicking a link would be an idea... Under what category would you place SMILES strings at the end?

I'll try to see how it looks in a smaller text size

Cacycle 21:37, 4 Nov 2004 (UTC)

SMILES will hopefully be implemented into Wikipedia at some stage. Until then I really think the CAS code will be sufficient. JFW | T@lk 23:51, 6 Nov 2004 (UTC)

I have moved the longer SMILES strings to the bottom into the Chemistry sections. I think the SMILES string make alot of sense if you want to create or recreate molecule images in your molecule editor. Copy and pasting the SMILES string is way faster and less prone to error than trying to draw the whole structure over and over again. The CAS number does not do this. Cacycle 00:52, 7 Nov 2004 (UTC)

Hmm, I'm not convinced this is actually pretty. Can't we simply link to ChemBank or something? JFW | T@lk 01:03, 7 Nov 2004 (UTC)

Psychopharmacology

Hey Cacycle, you seem to be into psychopharmacology. Could you pinpoint some useful articles on Wikipedia where I could learn more? Specifically interested in depression, but then psychosis etc also has my interest. JFW | T@lk 23:51, 6 Nov 2004 (UTC)

Okay. JFW | T@lk 01:03, 7 Nov 2004 (UTC)

Drug Organization

First I want to thank you for your contributions (especially images) in this area of wikipedia which needs much work. I have only been working on the wikidrug pages for a short while, but I have added some new pages and updated some others that were in dire need of updating, like Diisopropyltryptamine. (I am very interested in this particular drug and hope to soon better word some of the ideas on the page). Not many other wikipedians seem to be actively updating these pages, but I hope that nonetheless, an organizational heirarchy can be found for classifying drugs, particularly of the hallucinogenic variety. Official WikiProject Drugs/Categorization Talk Page

I believe that an essential dilemma exists in the overlap of some categories. While non-hallucinogenic drugs fit somewhat smugly into their individual template categories, not all phenethylamines are hallucinogenic, and not all tryptomines are hallucingenic, and other drugs that may have hallucinogenic qualities do not neccesarily fit other's definition of hallucinogens. There is great ambiguity in this area and I hope that we can work together to create a sense of clear and valid organization. I have posted on the talk pages of wikidrug project and hallucinogenic drug some criticisms/ideas. I think that it will probably become neccesary to delineate hallucinogens from drugs which cause hallucinations. Although this may sound counterintuitive, the latter group is far more broad than the former, which has created a large degree of annoying ambiguity of definition. The implications of this have been seen in the categorization of the dissociative anaesthetics, for example. Where a widespread common belief contradicts an accepted medical categorization, I believe that the medical category should hold precedent over the commonly held belief. To categorize drugs as hallucinogens actually goes against the official standard that the WikiDrugProject is based on, the ATCCS. Obviously, there is much discussion that this topic mandates, and I hope to hear some ideas. Formalizing the presentation of wikipedia articles is of utmost importance to us all, of course, and I hope to have this issue cleared up. Thanks. Flying Hamster 22:46, 7 Nov 2004 (UTC)

This is in regards to drug category overlap. I've been working on a drug chart for the major common psychoactives, and where they fall within three intersecting areas of Stimulant, Depressant and Hallucinogen). Please take a look at it on my Talk page (User_talk:Thoric) --Thoric 17:25, 12 Nov 2004 (UTC)

3C-I

3C-I: Phenethylamine or psychedelic amphetamine? Is it okay to call 3C-I a phenethylamine, or is it better termed a psychedelic amphetamine? Shulgin kind of lumped it all together as phenethylamines in his book, but sometimes I wonder if I feel completely correct calling MDMA a phenethylamine. Then again, I guess they could be considered phenethylamines with an alpha-methyl group. Do you know which is more proper or correct, anyway?

Also, any idea why Shulgin didn't add some of the other 3c compounds? Assumably there should be Br/I versions of the escaline as well, which would both be theoretically more potent than the ethoxy group...Shulgin could easily have added many more psychedelic amphetamines to Pihkal, and I always wonder why he didn't. Was it because 3,5-DIMETHOXY-4-BROMOAMPHETAMINE didn't show much promise? --Nuke

The use of phenethylamines vs. hallucinogenic phenethylamines has to do with the ongoing wikipedia drug classification project vs. classification by chemical classes (most phenethylamines are not psychedelic / hallucinogenic). It's perfectly ok to call 3C-E an amphetamine in the text, but for categorization purposes it doesn't make that much sense to add one more subcategory to the scheme, at least as long as the number of entries are manageable.

Shulgin has simply put everything he had synthesized and tested at that time into his book. Beside that it might a bit more difficult to synthesize that derivative.

I think Shulgin just ran out of space... he did cover a very large quantity of phenethylamines... Flying Hamster 15:23, 19 Nov 2004 (UTC)

Admin rights abuse

I'd like to know why do you abuse your admin rights and delete correct chemical formulas and replace them with your own versions. Thanks, --Mykhal 22:09, 2 Dec 2004 (UTC)

Actually I don't have (and never had) admin rights. Several weeks ago there must have been a software glitch and several of my uploads during that night did replace existing images. I'm sorry for that, it was not my intent.

As for redrawing existing images - that's how wikipedia works. If I see something to improve I will do it, even if these changes seem very minor to others. If you think it was a bad contribution then feel free to revert it and/or discuss it with me. BTW, as I told you before, I like the way you draw your chemical structures and really appreciate your work here :-)

Cacycle 20:13, 3 Dec 2004 (UTC)

Chemical data

Hello. Please keep on your mind, that Wikipedia is not encyclopedia for chemists. Doy you think it is necessary to have in the infobox long obscure systematic names or even more of them, and the long SMILES strings, which are nonsense for the absolute majority of Wikipedia readers, so these should be somewhere in the text, rather hidden. --Mykhal 22:09, 2 Dec 2004 (UTC)

If we have an article about a chemical compounds I think it is absolutely necessary to have some kind of systematic name in there beside the trivial name. Often there are also established mixed trivial/systematic names. Most names I have added are relatively short, Ascorbic acid might be a border case. I agree that systematic names for more complex compounds or (bio)polymers make no sense.

After much thinking about it I would say that the SMILES string is very important. It allows to copy and paste a chemical structure into the molecule editor without redrawing the molecule over and over again from scratch, thereby eliminating sources of errors, especially for non-chemists and beginners. Just think about students who need a chemical structure for a talk or a term paper. The resolution of the Wikipedia structure images might be too low for that. Moreover, there might (hopefully) be a Wikipedia feature in the future to automatically display SMILES structures.

Sure, Wikipedia is not for chemists, but if we discuss chemical compounds we can and should add relevant chemical information. All the existing types of data boxes are a way to keep such data in one place without clogging the main text. Nobody has to read all those values and complex names, but some people are looking exactly for that.

Cacycle 20:55, 3 Dec 2004 (UTC)

Sorry, but I disagree- Wikipedia is for chemists, as well as historians, musicians, etc. If you mean "Chemistry articles should not require a PhD in chem to read them", then I agree. But that is not the same as saying "PhD chemists should not find any value in Wikipedia chem articles". (After all, there are 60-100,000 PhD chemists in the USA alone!) Remember that someone looking on Wikipedia for an article on praseodymium(III) chloride is likely to be someone who at least knows what praseodymium is. When I write pages such as copper(I) chloride (my last entry), I aim it at a range of people, and try to provide valuable information for all. There may be a high school student writing a term project on copper, there may be a college Computer Science student with an interest in chemistry, or there may be an organic chem (post)graduate student whose supervisor has asked them to consider using CuCl in a reaction. I like to think that all of those people would find that page valuable. In turn I understand that if I (a chemist with wide interests) look at a page on an obscure mineral or an obscure philosophy, there may be parts of it I don't understand- but that's fine with me, as long as I can get the basic information. So let's try and "layer" these articles- include information at a basic, intermediate and moderately advanced level, so as to make it useful to as many people as possible. Let's include links, so if someone wants to understand what a Lewis acid is, they can find it. But let's make sure the pages provide valuable information to all of the likely readers- not just the non-chemists.

Walkerma 19:22, 31 Jan 2005 (UTC)

Admin rights abuse

I'd like to know why do you abuse your admin rights and delete correct chemical formulas and replace them with your own versions. Thanks, --Mykhal 22:09, 2 Dec 2004 (UTC)

Actually I don't have (and never had) admin rights. Several weeks ago there must have been a software glitch and several of my uploads during that night did replace existing images. I'm sorry for that, it was not my intent.

As for redrawing existing images - that's how wikipedia works. If I see something to improve I can do it, even if these changes seem very minor to others. If you think it was a bad contribution then feel free to revert it and/or discuss it with me. BTW, as I told you before, I really like your structures and really appreciate your work here :-)

I am sorry for the allegation. I had on mind the Image:Anandamide.png, which have been replaced by you, and the original image have disappeared from history. I recall, that something similar happened to me, about twice. It is probably wikipedia bug. But, indeed, my structure was correct, probably you did not like the shorthand form -(CH₂)₃- in it, but it was my intention. Sometimes it is better for clarity (especially when longer chains are present), to combine skeletal formula with such "labels". Another case may be the methoxy group. It should be written -OCH₃, and not -O- . But it is just my own opinion. --Mykhal 11:49, 16 Dec 2004 (UTC)

THC stereochemistry

Hello. Could you please revise your Image:THC structure.png ? It seems it is the wrong enantiomer. --Mykhal 01:06, 17 Dec 2004 (UTC)

Thank you for that observation. I have checked my literature. The stereochemistry was taken from from http://leda.lycaeum.org/?ID=90 and http://chemfinder.cambridgesoft.com/. But both sources are indeed wrong. I have corrected the THC structure as well as the related structures of THV, CBD, and CBDV.

Cacycle 11:31, 17 Dec 2004 (UTC)

( My opinion is supported by the MDL Crossfire (Beilstein), CAS (via ACS SciFinder), The Merck Index 13, WHO Mednet, NIH NLM ChemIDPlus, and also by primary literature: DOI:10.1016/S0040-4039(00)90646-4. Unfortunately, CS ChemFinder, again, has the wrong structure. --Mykhal 11:18, 17 Dec 2004 (UTC) )

DNAbasePairing.png

Could you add a comment to Image talk:DNAbasePairing.png saying what you found wrong with the image (unless you're about to upload a corrected version)? Thanks. -R. S. Shaw 04:25, 2005 Jan 24 (UTC)

Displayed formulae / How to draw chemical structures

What do you use to create these? I am looking for some good software on which to make good displayed/strucural formulae. --Oldak Quill 19:54, 24 Jan 2005 (UTC)

I've been using ChemDraw and Photoshop, but that's overkill. The trick is to increase the size to 300% or so, to export as an image, and to sample the image size down again, at least as long as the molecule editor does not give acceptable results alone. See also molecule editors and Mykhal's page for his technique. Cacycle 21:20, 24 Jan 2005 (UTC)