User talk:Fuse809

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Welcome to Wikimedia Commons, Fuse809!

-- 08:00, 24 January 2012 (UTC)

File tagging File:Pethidine3Dan.gif[edit]

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SamuelFreli (talk) 02:05, 10 May 2013 (UTC)Reply[reply]

File tagging File:Lysergide3Dan.gif[edit]

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SamuelFreli (talk) 02:05, 10 May 2013 (UTC)Reply[reply]

File tagging File:Nicotine3Dan.gif[edit]

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SamuelFreli (talk) 02:06, 10 May 2013 (UTC)Reply[reply]

File tagging File:Morphine3Dan.gif[edit]

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SamuelFreli (talk) 02:06, 10 May 2013 (UTC)Reply[reply]

File tagging File:Fentanyl3Dan.gif[edit]

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SamuelFreli (talk) 02:06, 10 May 2013 (UTC)Reply[reply]

File tagging File:Fentanyl's 3D molecular structure.gif[edit]

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SamuelFreli (talk) 02:06, 10 May 2013 (UTC)Reply[reply]

3d animations[edit]

After some verifications, it seems you really created those files. Could you just add the software name (I think it's QuteMol, so it's open source, but they stil ldeserve a little credit).

If you could just add that, I think we can simply remove the authorization request template.

Thank you! --SamuelFreli (talk) 14:16, 11 May 2013 (UTC)Reply[reply]

Tip: Categorizing images[edit]

Afrikaans  العربية  беларуская (тарашкевіца)  বাংলা  català  čeština  dansk  Deutsch  Deutsch (Sie-Form)  Ελληνικά  English  Esperanto  español  فارسی  suomi  français  galego  עברית  magyar  íslenska  italiano  日本語  ქართული  한국어  македонски  മലയാളം  norsk bokmål  Plattdüütsch  Nederlands  norsk  polski  português  português do Brasil  română  русский  sicilianu  slovenčina  slovenščina  српски / srpski  svenska  Türkçe  українська  Tiếng Việt  中文(简体)‎  中文(繁體)‎  +/−


Hello, Fuse809!
Tip: Add categories to your images

Thanks a lot for contributing to the Wikimedia Commons! Here's a tip to make your uploads more useful: Why not add some categories to describe them? This will help more people to find and use them.

Here's how:

1) If you're using the UploadWizard, you can add categories to each file when you describe it. Just click "more options" for the file and add the categories which make sense:

Uploadwizard-categories.png

2) You can also pick the file from your list of uploads, edit the file description page, and manually add the category code at the end of the page.

[[Category:Category name]]

For example, if you are uploading a diagram showing the orbits of comets, you add the following code:

[[Category:Astronomical diagrams]]
[[Category:Comets]]

This will make the diagram show up in the categories "Astronomical diagrams" and "Comets".

When picking categories, try to choose a specific category ("Astronomical diagrams") over a generic one ("Illustrations").

Thanks again for your uploads! More information about categorization can be found in Commons:Categories, and don't hesitate to leave a note on the help desk.

EugeneZelenko (talk) 16:03, 14 December 2013 (UTC)Reply[reply]

Cocaine Picture[edit]

Where is the Nitrogen molecule in your cocaine picture? I don't see it there normally it is colored blue. 50.80.153.173 23:02, 17 February 2014 (UTC)Reply[reply]

Nitrogen geometry in File:Metazimole3Dan.gif[edit]

You have the nitrogen that is attached to (not part of) the ring as trigonal–planar with a plane rotated 90° from the plane of the ring. At least one of those two details is likely not correct. The only common reason an en:amine tends to be planar rather than tetrahedral is if it is conjugated to an adjacent part of the structure, but a en:conjugated system nearly always requires co-planarity of all its parts. DMacks (talk) 17:29, 21 April 2014 (UTC)Reply[reply]

Unrelatedly, on the image-description page, you wrote that it is "Structure of" (didn't fill in the blank on some template/standard form?). I spot-checked a few other recent uploads of yours, and they all have the same situation. DMacks (talk) 17:31, 21 April 2014 (UTC)Reply[reply]

I was referred to https://commons.wikimedia.org/wiki/Commons:Upload/Chemistry as the upload form by en:User:Leyo as he had complained about me uploading my files to the en Wiki as they were transferred here. I only filled in the empty fields at the upload link I just shared. As for metamizole; does this image satisfy these constraints?

Metamizole3DanJ.gif

Fuse809 (talk) 00:17, 22 April 2014 (UTC)Reply[reply]

Frame #4 in that is an excellent example of the wrong geometry of the non-ring nitrogen. DMacks (talk) 03:01, 22 April 2014 (UTC)Reply[reply]

I must have horrible vision because I see 120° angles, not 90°. Fuse809 (talk) 04:24, 22 April 2014 (UTC)Reply[reply]

Look!

MetamizoleTrig.jpg

It's trigonal planar i.e. 120°! Fuse809 (talk) 04:38, 22 April 2014 (UTC)Reply[reply]

It's trigonal–planar in your image, I agree. That's exactly what I said was (one of possibly two) mistakes. Again, amines are tetrahedral--that's a pretty basic concept from intro chemistry courses. DMacks (talk) 14:21, 22 April 2014 (UTC)Reply[reply]
Or alternatively, the planar N needs to be 0° (coplanar) with the ring itself (not twisted at all (for example, in the X-ray of the en:Ampyrone parent structure according to doi:10.3390/molecules18010877). DMacks (talk) 16:50, 22 April 2014 (UTC)Reply[reply]

I've performed structure optimisation with Avogadro and got this PDB; show me what's wrong in it as I've done repeated optimisations with en:Avogadro and en:Jmol and I can't achieve tetrahedral geometry. Fuse809 (talk) 02:13, 23 April 2014 (UTC)Reply[reply]

The reason is that the lone pair has formed a pi bond with the 5-member ring (i.e. it's become conjugated). Fuse809 (talk) 05:11, 23 April 2014 (UTC)Reply[reply]

Your PDB has the N lone-pair oriented not in a direction that can conjugate to the ring. That was the other option for the mistake I originally mentioned. Again, if the N is planar, that plane must align with the plane of the ring, not be twisted, in order to conjugate (the methyl and the C of the CH2 going to the sulfonic acid must be in the same plane as the ring, not one on each face). Simple geometric optimization is sensitive to starting point, which is why "our minimizations" need to be sanity-checked from other sources. It's easy to get benzene rings interlinked, etc. It's too easy to overstate one's confidence in how something is by making it a high quality image--don't want to mis-lead our readers that there is any actual verifiable basis for this 3D geometry. By moving atoms from the minimized PDB to make it tetrahedral, I could get it to remain that way in minimization. I can converge on 4 different geometries ("which face of the ring has the methyl vs the methanesulfonic acid" and to a lesser extent "lone-pair pointed towards carbonyl vs methyl" on the ring). Without published source, I can't accept any of them as the "right one", especially regarding the ring-faces. Presumably one of them is most important for binding; presumably one of them is most common in solution or crystal. And I can also converge on two different planar forms, thanks to conjugation, depending which group on the N goes which way (again, I'd want a ref to choose between them, let alone between planar and tetrahedral). DMacks (talk) 04:24, 27 April 2014 (UTC)Reply[reply]

Would you care to provide me with a PDB file that does work for you? Fuse809 (talk) 04:50, 27 April 2014 (UTC)Reply[reply]

Would en:PubChem's SDF file satisfy your requirements for something published? Fuse809 (talk) 06:48, 27 April 2014 (UTC)Reply[reply]

Here's a published journal article with its structure (doi:10.1107/S0567740879004271. Based on this geometry, the following coordinates should be valid
38
BVP86/cc-PVDZ scf done: -1369.314862
 C     0.634952    10.049072     4.900129
 C    -0.038364     9.052812     5.625610
 C    -0.843603     9.404086     6.721280
 C    -0.967888    10.746974     7.078721
 C    -0.317360    11.745954     6.347432
 C     0.482122    11.389915     5.258069
 N     0.088512     7.682548     5.283073
 N     0.524862     7.332867     3.979484
 C     1.016111     6.033439     4.052906
 C     1.037214     5.613638     5.356904
 C     0.456058     6.652593     6.201473
 C    -0.418749     7.686282     2.908454
 C     1.415171     5.281438     2.830834
 N     1.587824     4.410206     5.852441
 C     0.695266     3.536091     6.539780
 S     0.466632     1.963130     5.547604
 O     1.708338     1.174668     5.559744
 O     0.313685     6.699922     7.422867
 C     2.964673     4.465074     6.365693
 O    -0.210611     2.273661     4.290449
 O    -0.634313     1.159020     6.505778
 H    -0.141454     0.406631     6.889481
 H    -1.345054     8.622837     7.287776
 H    -1.589369    11.013825     7.934553
 H    -0.429995    12.793897     6.626878
 H     1.005549    12.158525     4.687515
 H     1.289838     9.765864     4.076298
 H    -1.364716     7.127508     2.998793
 H     0.053315     7.462436     1.945681
 H    -0.625790     8.761093     2.953974
 H     0.547989     5.057675     2.191339
 H     2.145811     5.841566     2.228931
 H     1.854760     4.324136     3.132627
 H    -0.315695     3.946934     6.648080
 H     1.067111     3.196537     7.517244
 H     3.601787     4.973633     5.631670
 H     3.344097     3.442734     6.490780
 H     3.030898     5.004553     7.327684
Do you accept this geometry, DMacks? Brenton (talk|email) (I automatically watch all pages I edit) 08:23, 4 July 2014 (UTC)Reply[reply]
Published crystal structures are a good source. The fact that it contradicts many of the geometric assumptions you had previously made (vs agreeing with some of my comments) is a good indication that you should re-examine other diagrams you have made and (at least!) cite them as such. That way readers can know they are not specifically based on reliable sources. DMacks (talk) 15:23, 19 July 2014 (UTC)Reply[reply]
I would agree with you but it takes forever for one to find crystal structures, in my experience. Why this crystal structure required me to ask other more experienced chemists to find it, why you didn't even find it and you're the chemist out of us two. I am merely a pharm student. Hence I favour using PubChem and ChemSpider's structures. Despite this I am glad you brought this up, as I am 1/4 Jew so I understand the danger of blind conformity, so thank you. Brenton (talk) 23:09, 19 July 2014 (UTC)Reply[reply]

The factual accuracy of the chemical structure File:Nalbuphine2DCSDW.svg is disputed[edit]

Dispute notification The chemical structure File:Nalbuphine2DCSDW.svg you uploaded has been tagged as disputed and is now listed in Category:Disputed chemical diagrams. Files in this category are deleted after one month if there is no upload of a corrected version and if there is no objection from the uploader or other users. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload a corrected version or simply allow the file to be deleted.

In all cases, please do not take the dispute personally. It is never intended as such. Thank you! --Rhadamante (talk) 00:49, 31 May 2014 (UTC)Reply[reply]


File source is not properly indicated: File:PubMed Health search for Wikipedia.png[edit]

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Túrelio (talk) 08:22, 21 June 2014 (UTC)Reply[reply]

US gov website not so rarely use not-own images (per fair use), whereby such images do not become PD-US-Gov and are not allowed on Commons. So, you need to provide the exact source, from which you created the screenshot and you need to find out the original source/author of the included images. --Túrelio (talk) 08:25, 21 June 2014 (UTC)Reply[reply]

File source is not properly indicated: File:PubMed search for Wikipedia.png[edit]

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File:PubMed Health search for Wikipedia.png[edit]

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JuTa 07:05, 29 June 2014 (UTC)Reply[reply]

Incorrect structure, recommend pulling from Wikipedia[edit]

Go to the Tetracycline article, [1], and see the image that is now presented there. Your representation of tetracycline, File:Tetracycline2DCSD.svg, which was replaced, is non-standard (not the way any knowledgeable organic chemist would depict it). It is simply incorrect and unacceptable as an image at WP. In particular, its presentation of a dashed line projecting from a planar olefin, depiction of the stereochemistry at the ring junctions, omission of hydrogens at chiral centers, presentation of dashed bonds within rings, etc., are non-standard. The image in place now is correct, and standard (though in a different pose). I would strongly recommend you remove File:Tetracycline2DCSD.svg from Wikimedia Commons and in the places it is in use (or replace it with one that you create, that looks like the one that is currently in the article). This presentation, however sourced, is not how it is correctly done. Le Prof Leprof 7272 (talk) 17:49, 1 July 2014 (UTC)Reply[reply]

Sorry, I didn't notice this. Thank you for your feedback. So I have taken ChemSpider's mol file and used that to fix this problem. I will fix accordingly, although I can't remove the file as I'm not an administrator. So I will re-upload at here. But, I suggest for your future reference that instead of editing the description page with your input you edit the talk page instead as that's what it's there for. Plus you can add this to the description page:
{{Disputed chem}}
in order to prevent people from using it. Consequently I will move your comments to the talk page and flag it for deletion. Brenton (talk|email) (I automatically watch all pages I edit) 01:09, 2 July 2014 (UTC)Reply[reply]
ps. if you want to link to the English Wikipedia you just need to type en:pagename in double square brackets ([[]]). e.g. tetracycline would be: tetracycline. Brenton (talk|email) (I automatically watch all pages I edit) 01:20, 2 July 2014 (UTC)Reply[reply]
Thank you for response, and for technical advice on Wikipedia formats/tools. Le Prof Leprof 7272 (talk) 00:58, 4 August 2014 (UTC)Reply[reply]

The factual accuracy of the chemical structure File:Etomidate3DanJ.gif is disputed[edit]

Dispute notification The chemical structure File:Etomidate3DanJ.gif you uploaded has been tagged as disputed and is now listed in Category:Disputed chemical diagrams. Files in this category are deleted after one month if there is no upload of a corrected version and if there is no objection from the uploader or other users. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload a corrected version or simply allow the file to be deleted.

In all cases, please do not take the dispute personally. It is never intended as such. Thank you! --DMacks (talk) 06:58, 2 July 2014 (UTC)Reply[reply]


File:Cyclopamine2DACS.svg[edit]

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DMacks (talk) 16:47, 28 July 2014 (UTC)Reply[reply]

In re: non-attributed, computationally ill-defined 3D images, spinning or otherwise[edit]

Please see discussion at the Wikiproject:Pharmacology, [2], for reasons and supporting opinions about this misuse of chemical information. Le Prof Leprof 7272 (talk) 00:55, 4 August 2014 (UTC)Reply[reply]

I don't know why you are directing me there as in case you didn't read the messages that came before you I had already commented on Mad's comments. Brenton (talk) 01:08, 4 August 2014 (UTC)Reply[reply]

File:Thalidomide2DCSD.svg[edit]

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DMacks (talk) 19:42, 28 September 2014 (UTC)Reply[reply]


The factual accuracy of the chemical structure File:Prinomastat2DACS.svg is disputed[edit]

Dispute notification The chemical structure File:Prinomastat2DACS.svg you uploaded has been tagged as disputed and is now listed in Category:Disputed chemical diagrams. Files in this category are deleted after one month if there is no upload of a corrected version and if there is no objection from the uploader or other users. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload a corrected version or simply allow the file to be deleted.

In all cases, please do not take the dispute personally. It is never intended as such. Thank you! --Ed (Edgar181) 17:10, 28 November 2014 (UTC)Reply[reply]



The factual accuracy of the chemical structure File:Maitansine2DCSD.svg is disputed[edit]

Dispute notification The chemical structure File:Maitansine2DCSD.svg you uploaded has been tagged as disputed and is now listed in Category:Disputed chemical diagrams. Files in this category are deleted after one month if there is no upload of a corrected version and if there is no objection from the uploader or other users. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload a corrected version or simply allow the file to be deleted.

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Copyright status: File:Ifosfamide2DCSD.svg[edit]

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JuTa 00:14, 26 April 2015 (UTC)Reply[reply]

Copyright status: File:Ifosfamide racemate2DCSD.svg[edit]

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JuTa 00:14, 26 April 2015 (UTC)Reply[reply]

Rifampicin3Dan.gif[edit]

Dear Fuse809, how do you create gif images of molecular structures like you have for Rifampicin3Dan.gif? I find them really useful. Thanks, Originalwana (talk) 13:56, 4 November 2015 (UTC)Reply[reply]

Rifampicin3Dan.gif
This one was created using QuteMol. All ya have to do is get an acceptable PDB or SDF file (I think for this one I would have used PubChem's 3D SDF file) and load it in QuteMol. I haven't used QuteMol in a while though, so I can't remember much specifics. Brenton (talk) 13:59, 4 November 2015 (UTC)Reply[reply]
ThanksOriginalwana (talk) 10:36, 6 November 2015 (UTC)Reply[reply]

File:Pethidine-PM3-based-on-xtal-1974-3D-balls.svg[edit]

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Leyo 23:00, 23 April 2016 (UTC)Reply[reply]

File:Alazocine1.svg[edit]

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Leyo 12:04, 26 April 2016 (UTC)Reply[reply]

File:Selenocysteine2DACS.svg[edit]

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DMacks (talk) 13:53, 27 September 2016 (UTC)Reply[reply]

File:Metformin3Dan.gif[edit]

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DMacks (talk) 18:48, 5 November 2016 (UTC)Reply[reply]

File:O-desmethyltramadol racemate2DCSD.svg[edit]

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DMacks (talk) 15:27, 28 November 2016 (UTC)Reply[reply]

File:MetamizoleTrig2.jpg[edit]

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Leyo 09:50, 21 August 2017 (UTC)Reply[reply]

File:Ibogaine2DACS.svg[edit]

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DMacks (talk) 08:36, 19 October 2017 (UTC)Reply[reply]

The quality of the chemical structure File:Tiletamine-ball-and-stick-model.png is disputed[edit]

Dispute notification The chemical structure File:Tiletamine-ball-and-stick-model.png you uploaded has been tagged as and is now listed in Category:Low quality chemical diagrams. Files in this category might be deleted after one month if there is no upload of an improved version, if there is no objection from the uploader or other users, and if a better version exists. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload an improved version or simply allow the file to be deleted.

In all cases, please do not take the dispute personally. It is never intended as such. Thank you! --DMacks (talk) 15:43, 24 October 2017 (UTC)Reply[reply]


I like the 3D diagrams for small molecules, but your choice of lighting or perspective makes some 3D details hard to see. Maybe using a lighter gray (and generally desaturating the colors?) for carbon, or somehow else making it more visually "spherical" (rather than flat black circle) would help. For example, compare File:Tiletamine-ball-and-stick-model.png to File:Tiletamine-3d-sticks.png. DMacks (talk) 15:43, 24 October 2017 (UTC)Reply[reply]

I don't get what the problem is but to placate you I've uploaded two revisions with lighter carbon colours. I can see the 3D geometry fine. I've tried to do everything to placate you (like using Avogadro to optimized the geometry using crystal structures where possible) and others on Commons with my latest uploads but still there's a problem. But I suppose I should be happy for the opportunity to improve my work. Brenton (talk) 16:16, 24 October 2017 (UTC)Reply[reply]

The factual accuracy of the chemical structure File:Salvinorin A3DanJ.gif is disputed[edit]

Dispute notification The chemical structure File:Salvinorin A3DanJ.gif you uploaded has been tagged as disputed and is now listed in Category:Disputed chemical diagrams. Files in this category are deleted after one month if there is no upload of a corrected version and if there is no objection from the uploader or other users. Please discuss on the file talk page if you feel that the dispute is inappropriate. If you agree with the dispute, you can either upload a corrected version or simply allow the file to be deleted.

In all cases, please do not take the dispute personally. It is never intended as such. Thank you! --Mykhal (talk) 08:32, 22 November 2018 (UTC)Reply[reply]


Comment on British vs. American spelling differences[edit]

Re: Defence Defense Labour Labor British American spelling by country.svg, just in case you were wondering. Getsnoopy (talk) 23:32, 10 May 2020 (UTC)Reply[reply]

File:Ubuntu Kylin 17.10 English.png[edit]

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File:PubMed Health systematic reviews selection.png[edit]

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P 1 9 9   18:22, 7 May 2021 (UTC)Reply[reply]

File:Nalbuphine2DCSDF.svg[edit]

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Marbletan (talk) 15:46, 29 November 2021 (UTC)Reply[reply]

File:Etorphine2DCSD.svg[edit]

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Marbletan (talk) 17:50, 25 April 2022 (UTC)Reply[reply]

File:7-PET3DanJ.gif[edit]

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Innerstream (talk) 21:35, 16 July 2022 (UTC)Reply[reply]

Oxymorphone Gif[edit]

Saw your Oxymorphone GIF on page Oxymorphone, was pretty sweet. Rock on! I think I did one on Chromium Picolinate years back (Chromium(III) picolinate) under the Biochemistry section. Anyway see you around the comp chem world. Mplanine (talk) 12:30, 4 November 2022 (UTC)Reply[reply]