User talk:Boghog/Archive 4

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Happy New Year

Hey Boghog, I hope that you and your family have a Happy New Year. :--Literaturegeek | T@1k? 10:03, 2 January 2010 (UTC)

Hej LG, thanks and likewise I wish you and yours all the best in the New Year! Boghog (talk) 10:53, 2 January 2010 (UTC)

• Happy New 2010, all the best for you, thanks for always helping out! Left a note at the talkpage of LMNA. ^_^ Cheers, --CopperKettle 13:04, 3 January 2010 (UTC)

Protein and gene names

Hope you had a good start into the new year. Besides, I only wanted to ask what you think of my considerations and questions regarding protein and gene names. Cheers, ἀνυπόδητος (talk) 20:21, 16 January 2010 (UTC)

Likewise, I hope the new year is treating you well. I have not forgotten about our discussion. I do plan to tweak the opening sentences once I am back into a "programming mode". Give me a week or two. All the best. Boghog (talk) 20:28, 16 January 2010 (UTC)

Take your time. I'll leave the gene/protein articles in peace for now (no page moves, no changing of opening sentences, no creating of redirects) until you and BogBot are finished, or until you ask for assistance. Best regards, ἀνυπόδητος (talk) 20:39, 16 January 2010 (UTC)

3-hydroxyacyl-CoA dehydrogenase

There appear to be two articles with the same enzyme name:

• 3-hydroxyacyl-CoA dehydrogenase
• 3-Hydroxyacyl CoA dehydrogenase

Should the second article be merged into the first? --Robert.Allen (talk) 01:23, 20 January 2010 (UTC)

Yes, definitely. Thanks for identifying and merging these two duplicate articles. Cheers. Boghog (talk) 06:08, 20 January 2010 (UTC)

Immunoglobulin domains

Hi again! Do you know whether an immunoglobulin fold is the same as an immunoglobulin domain? Looks like it to judge from the Pfam boxes, I'm just irritated by the term "Immunoglobulin-like domain" in the latter article. --ἀνυπόδητος (talk) 10:52, 20 January 2010 (UTC)

I think the difference between a fold and a domain is that the former is a type of tertiary structure while the later in addition is autonomously stable. In this context, I think a immunoglobulin domain and fold refer to the same tertiary structure. Therefore I have taken the liberty of merging them. Thanks for catching this. Cheers. Boghog (talk) 21:47, 20 January 2010 (UTC)

Thanks --ἀνυπόδητος (talk) 17:21, 21 January 2010 (UTC)

Maor Levi

Hello. Could you possibly do me a favor? I've been trying to start this (it's red I know but click it anyway) article for months. I've requested unprotection 2-3 times but for whatever reason nobody ever does anything about it. Maor Levi is one of my favorite electronic artists of all time and I'd like to give him a place here on Wikipedia. Here's his Last.fm profile. If you can do so thanks a ton! el3ctr0nika (Talk | Contribs) 04:59, 1 February 2010 (UTC)

Sorry, but I am not an administrator therefore I cannot create this article either. If he fulfills the WP:BAND or WP:COMPOSER requirements, I would suggest creating a stub in your user space. Make sure to include at least one reliable source that establishes Maor Levi's notability. Then contact User:Cobaltbluetony with a link to your stub and request that the block be removed. Cheers. Boghog (talk) 07:23, 1 February 2010 (UTC)

Ohh I thought you were an admin for some reason. Sorry lol. And thanks I'll look into that. el3ctr0nika (Talk | Contribs) 22:58, 1 February 2010 (UTC)

Beta clamp

Tri-spammed to Boghog2, ClockworkSoul and TimVickers

Could someone else check out Beta clamp? I suggested redirecting it to DNA clamp at MCB talk but I don't want to be judge, jury and executioner to an article written in good faith by a new contributor. Adrian J. Hunter^{(talk•contribs)} 01:48, 31 January 2010 (UTC)

Thanks for the note. I agree with you that the beta clamp article should be merged into DNA clamp. I have added merge tags to the two articles and started a discussion here. In addition, I have started to edit both articles to get them ready for a merge. Cheers. Boghog (talk) 12:44, 31 January 2010 (UTC)

Thanks for that, Boghog. Sorry I don't have more time right now to help with the merge. Adrian J. Hunter^{(talk•contribs)} 03:57, 4 February 2010 (UTC)

Gene vs. protein

Hi! Just saw that you nominated Nyctalopin for deletion but I have to admit I don't understand the reason. Because NYX_(gene) should be moved to nyctalopin? What's the official wiki policy? Should one name the main article after the gene or the protein? It is quite mixed now as far as I can see. Usually the article is named after the gene but about the protein. Thanks, Panoramix303 (talk) 20:17, 12 February 2010 (UTC)

Hi Panoramix303! I don't think there is any official policy concerning whether Gene Wiki pages should be named after the protein or the gene. In this particular case however, nyctalopin is both the official HUGO gene and UniProt protein name. In addition, there is an unofficial preference that the full gene/protein name be used if the full name is concise:

• Preference should be given to gene names over symbols when a clear and succinct name is available.

Cheers. Boghog (talk) 22:48, 12 February 2010 (UTC)

Thank you

		The Chemistry Star
		I just wanted to let you know that all your contributions to chemistry articles has not gone unnoticed. Thank you for all your efforts at improving articles in this corner of Wikipedia. -- Ed (Edgar181) 20:43, 24 February 2010 (UTC)

Thanks! Much appreciated. That is certainly a cool looking carbocycle and homoaromatic to boot. Returning to my roots I guess. Cheers. Boghog (talk) 21:32, 24 February 2010 (UTC)

Genetic code

I have re-instated it - on hold for seven days. There is a lot of work to be done. Jezhotwells (talk) 01:54, 27 February 2010 (UTC)

Thanks. I agree that the article needs some work and I will try to address your concerns over the next several days. Cheers. Boghog (talk) 08:17, 27 February 2010 (UTC)

BRAF (gene)

Wow, we did a good job on that entry. Just compare the January version with the latest one. Just in time, too. We got >4,000 hits after that New York Times story. --Nbauman (talk) 06:20, 3 March 2010 (UTC)

This one hits home since I recently lost a friend to melanoma. Thanks for your help in making the article more accessible to the general public. I didn't realize it was getting so many hits. Boghog (talk) 06:24, 3 March 2010 (UTC)

In the revision history http://en.wikipedia.org/w/index.php?title=BRAF_(gene)&action=history, click on "Page view statistics" and you'll get your dopamine surge. --Nbauman (talk) 18:48, 3 March 2010 (UTC)

DYK nomination of Cereblon

Hello! Your submission of Cereblon at the Did You Know nominations page has been reviewed, and there still are some issues that may need to be clarified. Please review the comment(s) underneath your nomination's entry and respond there as soon as possible. Thank you for contributing to Did You Know! SusanLesch (talk) 00:44, 12 March 2010 (UTC)

DYK for Cereblon

On March 15, 2010, Did you know? was updated with a fact from the article Cereblon, which you created or substantially expanded. You are welcome to check how many hits your article got while on the front page (here's how, quick check ) and add it to DYKSTATS if it got over 5,000. If you know of another interesting fact from a recently created article, then please suggest it on the Did you know? talk page.

Materialscientist (talk) 06:03, 15 March 2010 (UTC)

File:Diosgenin.png missing description details

Dear uploader: The media file you uploaded as File:Diosgenin.png is missing a description and/or other details on its image description page. If possible, please add this information. This will help other editors to make better use of the image, and it will be more informative for readers.

If the information is not provided, the image may eventually be proposed for deletion, a situation which is not desirable, and which can easily be avoided.

If you have any questions please see Help:Image page. Thank you. Sfan00 IMG (talk) 12:04, 16 March 2010 (UTC)

RVD-Hpα

Hi Boghog2. I came across this recently discovered endogenous polypeptide agonist for CB₁ cannabinoid receptors and figured it was fairly significant seeing as all previous endogenous CB₁ agonists have been lipids. I don't suppose you could give us a hand with the data box for the page? As it is clearly better classified as a protein rather than a chemical or drug it should have a protein box, but I'm not sure what should go in there... Meodipt (talk) 00:11, 22 March 2010 (UTC)

Interesting question. To the best of my knowledge, we don't have any templates suitable for exactly this type of situation (a relatively small polypeptide derived from a larger protein). My suggestion which I have already implemented is to fill in the data for the full protein, but then specify that the polypeptide is a fragment derived from the full protein. This is a bit of a kludge, but unless we create a new template, this is the best solution that I can come up with. I hope this is adequate. Cheers. Boghog (talk) 08:05, 22 March 2010 (UTC)

Yeah that looks great, thanks. I suspect the number of short polypeptide fragments that turn out to have important physiological roles will become rather large over the next few years, so perhaps a new template will be needed at some stage! Meodipt (talk) 08:49, 22 March 2010 (UTC)

Thanks for welcome, help and advice

Hi Boghog2. Given lack of progress with the thymosin page over years I was surprised and delighted to find my beginner's efforts getting instant support. Am specially grateful re citations. Lots more to be done re remaining cut-and-pastes. And lots for me to learn re Wikipedia. Jgedwards (talk) 08:45, 24 March 2010 (UTC)

You are off to a great start! You definitely know the thymosin subject matter much better than I do. Let me know if you have any questions concerning formatting, linking, etc. Cheers. Boghog (talk) 19:27, 24 March 2010 (UTC)

Thymosin b15

Hi Boghog. Good to point up 15A and 15B. However, it probably needs to be included that in humans the proteins off A and B genes are identical. (Though silent diffs in coding sequence). Happens it was me who spotted there were two genes and pointed out to Bruce Zetter at Harvard Med. School. In due course the b15 story can take on board that the Harvard group have it as a possible clinical marker for aggressive prostate cancer.

May be a little while before I get the actin binding stuff dealt with Jgedwards (talk) 23:08, 24 March 2010 (UTC)

It is great to have an expert on board who knows the subject so throughly. Your input is exactly the kind of contribution that the Gene Wiki project is attempting to attract. Good catch on the close relationship of TMSB15A to TMSB15B. Perhaps these two articles should be merged into a single TMSB15 article. Boghog (talk) 06:14, 25 March 2010 (UTC)

CBS Domain

Thanks for the structure box on the CBS domain page! Much appreciated. Alexbateman (talk) 09:24, 26 March 2010 (UTC)

No problem. Glad that you liked the structure box. Cheers. Boghog (talk) 15:48, 27 March 2010 (UTC)

Selective glucocorticoid receptor agonist

Hey, thanks for your fine work with the SEGRA article! Any idea whether SEGRAs interact with membrane GRs? Cheers, ἀνυπόδητος (talk) 09:59, 30 March 2010 (UTC)

And thank you for your hard work in bring the SEGRA article to up to GA status. The whole area of membrane GRs and the non-genomic activities glucocorticoids is not very well documented for non-selective ligands and even less is known about whether SEGRAs can act through these pathways. My hunch is that as ligands are optimized to transrepress and not transactivate, the less likely these selective ligands are to signal through other pathways including membrane GRs. However I am not aware of any published evidence that would either support or refute such a claim. Cheers. Boghog (talk) 19:58, 30 March 2010 (UTC)

Thanks for pointing me to that discussion. Are you sure non-genomic effects are relatively unimportant – clinically, I mean? I've heard the opinion that the genomic mechanisms can't account for the fast action. (Give bethametasone drops in an inflamed eye and count to ten.) Sounds sensible, but of course is not citeable. Cheers, ἀνυπόδητος (talk) 13:09, 31 March 2010 (UTC)

OK, I have done some more reading and perhaps I have underestimated somewhat the importance of non-genomic actions of glucocorticoids. I have expanded the Glucocorticoid#Non-genomic section with another example (PMID 11815387). Also this PMID 11815387 paper is especially relevant since it shows that different glucocorticoids vary in their ability to signal through genomic vs nongenomic pathways (some signal through both while others signal only through one or the other pathways; caution: these are in vitro and not in vivo results; many compounds that look dissociated in vitro do not turn out to be dissociated in vivo.) Hence another ´possibility for a dissociated glucocoricoid would be one that signals only through the non-genomic pathway. Furthermore some SEGRAs may also have non-genomic activity, but again, I am not aware of any publications that demonstrate this. Cheers. Boghog (talk) 14:41, 1 April 2010 (UTC)

Thanks for taking all the trouble! So we'll have to wait until further investigation is published. Cheers --ἀνυπόδητος (talk) 11:10, 2 April 2010 (UTC)

Thymosin Peacock

Hi boghog Simplification OK and thanks for citation/punctuation. As a lecturer I sometimes got panned for use of metaphors. Don't actually agree that para was pure peacock, though. There's a big difference between starting with a specific protein and seeing what it can do, and pursuing an unknown factor and finding what it is after all. Maybe I'll try to write that more prosaically sometime. but priority has to be the multiple activities of b4. With promotion of hair growth, repair after heart attack, neurological function..... begins to read like "snake oil" - another metaphor to avoid! . You'll have gathered I did some edits having forgotten to sign in. Jgedwards (talk) 10:34, 2 April 2010 (UTC)

Opps! My aplogizes. I didn't realize that it was you. If I had, I would have been a little less WP:BOLD. I have very high respect for your experience and insight into the subject of thymosin and I do very much appreciate your contributions. At the same time, it may take a bit of time to get used to the writing style appropriate for Wikipedia. What you wrote was interesting and engaging and would be very appropriate for a review article in a scientific journal. In Wikipedia however one should "concisely state facts about a subject" and "not discuss the underlying literature at any length". So I hope you don't take the comments I made in the edit summary personally. In any case, please carry on! Your contributions have greatly improved the article. Cheers. Boghog (talk) 07:44, 3 April 2010 (UTC)

Hi boghog No call to apologise. I continue to value your help and advice, particularly re what is appropriate for Wikipedia. Latest is that I've received very positive feedback via email from the original discoverer of thymosins, who is also the pre-eminent world authority. He's provided me with a rich vein of further material relating to the biological activities and clinical/medical applications, the latter which will very likely be of interest to general readers. He would like me to Wikify it as appropriate rather than getting directly involved himself. I'm also working on some images of solved structures of thymosin bound to actin. I'm really enjoying this, but please don't hesitate to be WP:BOLD if I stray into inappropriate! Jgedwards (talk) 11:41, 4 April 2010 (UTC)

Lactoperoxidase

Hi. :) Since you seem to have done such a good job on that article, I just wanted to let you know that permission has not yet been verified, so contributions by the contributor who added the copied passages have been removed. I've done my best to salvage the content subsequently placed by you and User:Mary Foster, but I realize this is probably a set-back for the article. Sorry about that! I always hate to see content lost for copyright concerns. :/ Since this is far out of my field, I did want to let you know that the purge is complete. If and when you have a chance, I'd be grateful if you could take a look to make sure that my clumsy cleanup hasn't cost the article vital sense. (I know you probably would anyway, since you've been hanging out there for a while, but I did want to let you know. :)) --Moonriddengirl ^(talk) 21:31, 9 April 2010 (UTC)

No problem and thank you for so carefully recovering the material that was non-infringing. I was also concerned about the copyright violation and I had gone so far in writing Professor Harper for permission, but he never responded. Thanks for taking care of this. Cheers. Boghog (talk) 05:02, 10 April 2010 (UTC)

A lot of information is gone but I want to help restore it without copyright violations. Boghog, we can work together using a sandbox with the old version and manually remove all the copyright violations and restore all the missing content. After the sandbox is approved for the article then it can be added to the article. Some of my work is still lost. Mary Foster (talk) 03:33, 11 April 2010 (UTC)

Mary Foster noted that I had missed quite a bit of the copyright problem itself in cleanup. I've had another go but at her request have also restored for a few days the deleted material so that you can try to rewrite the material. Anyway, there's more information at Talk:Lactoperoxidase#More cleanup. --Moonriddengirl ^(talk) 12:20, 11 April 2010 (UTC)

Thanks for granting temporary access the original version. I will work with Mary Foster to restore the non-infringing material. I will also try round out the remainder of the article using some of the same citations but completely rewriting it so the new material doesn't infringe. Boghog (talk) 13:29, 11 April 2010 (UTC)

Thank you very much! If one of you could let me know when you're finished, I'll delete the temporary page. It will come up automatically for review after seven days. :) --Moonriddengirl ^(talk) 17:21, 11 April 2010 (UTC)

Boghog, would "Oral care" be more accurate? Mary Foster (talk) 20:05, 11 April 2010 (UTC)

Good suggestion. Please feel free to change it. Boghog (talk) 20:12, 11 April 2010 (UTC)

On my user page there may be some references you can use in the article. Mary Foster (talk) 21:12, 11 April 2010 (UTC)

OK, thanks. I think I have restored most of the important ones. However if there are some that I missed that you think are important, please by all means add them. I will try to incorporate text to go along with any additional citations you add. Cheers. Boghog (talk) 21:23, 11 April 2010 (UTC)

It would take a lot of time to sort all of them out. For now I added all the references. Mary Foster (talk) 21:31, 11 April 2010 (UTC)

Function and Applications needs to be summarized in the lede. Mary Foster (talk) 01:16, 12 April 2010 (UTC)

		The Copyright Cleanup Barnstar
		For going above and beyond to rescue Lactoperoxidase after copyright concerns led to the significant loss of content. Your extraordinary efforts are appreciated! Moonriddengirl (talk) 22:33, 12 April 2010 (UTC)

Thanks! Very much appreciated. Boghog (talk) 22:54, 12 April 2010 (UTC)

About the PDB

Hi! You're sure to know this — can you tell me whether the "structure weight" in entries like PDB: 1TTG​ means the glycoprotein (as opposed to the polypeptide alone)? Cheers, ἀνυπόδητος (talk) 09:25, 17 April 2010 (UTC)

I am an organic chemist, not a protein chemist nor structural biologist by training. Therefore I am not 100% percent sure myself, so I did some digging. It appears that "structure weight" refers to the entire structure including anything that is covalently attached to the polypeptide. Even though fibronectin is a glycoprotein, the 1TTG doesn't have any saccharides in the resolved structure. Hence it is not the best example. A better example is PDB: 1VSG​. The formula weight listed on the summary tab is 78863.09. On the chemistry tab are listed the formula weight weight of the polypeptide (38845.0) and of the three covalently attached saccharides (180.16 + 180.16 + 221.21). Since the structure is dimeric, the total weight is 2 X (38845.0 + 180.16 + 180.16 + 221.21) = 78853.06. The calculated totals differ by 10. Part of the difference is that six water molecules are removed in forming the glycoprotein from the saccharide and polypeptide components. But then the MW totals are off by 98. Calculation of biopolymer molecular weights from crystallographic structures gets complicated. What should one do with disordered residues that are present in the crystal but not resolvable by diffraction? What about protonation states, counter ions, post-translational modification and chemical degradation? Also crystal structures may be of just one domain from an entire protein, contain non-natural residues or sequences to make purification and crystallization easier. How accurate do you need these weights? Because proteins are often somewhat heterogenous in vivo, listing one exact MW can be misleading and in my opinion is not particularly useful. Cheers. Boghog (talk) 11:26, 17 April 2010 (UTC)

Thanks, I know I always get a good answer from you :-) Don't mind about a difference of 100 Daltons; I know it doesn't make much sense to be that accurate. My problem was that the German article about Monobodies, genetically altered fibronectin type III domains, states (or stated, as I will be correcting it) that they have 94 residues and 15 kDa, which doesn't really fit, especially as I can't find any evidence about Monobodies being glycoproteins or having some other structural elements besides the peptide chain. --ἀνυπόδητος (talk) 13:11, 17 April 2010 (UTC)

GPCRs Template

Hey. For Template:G protein-coupled receptors, what would you think of recategorizing the class A/rhodopsin-like section? I was thinking something like the following:

• Small molecules (5-HT, dopamine, adenosine, histamine, acetylcholine, cannabinoids, etc)
• Orphans (self-explanatory)
• Peptides (opioids, oxytocin, melanocortins, and so forth)
• Steroids (testosterone, estrogen, progesterone, etc)
• Others (sigma, whatever else)

Possibly a lipids section as well for cannabinoids and such instead of placing them in small molecules?

I'd do it myself but I'm not quite knowledgeable enough in this entire field.

el3ctr0nika (Talk | Contribs) 08:10, 20 April 2010 (UTC)

Hej! Yes, this template has grown over time and I think a reorganization of the template is long over due. There are a couple of ways of doing this. One possible way is listed here, but the number of subfamilies in that classification is probably too large for a template. Similar to what you have suggested is present here:

• "A phylogenetic tree of all human GPCRs" (PDF). Vassilatis DK, Hohmann JG, Zeng H, Li F, Ranchalis JE, Mortrud MT, Brown A, Rodriguez SS, Weller JR, Wright AC, Bergmann JE, Gaitanaris GA (2003). "The G protein-coupled receptor repertoires of human and mouse". Proc Natl Acad Sci USA. 100 (8): 4903–8. doi:10.1073/pnas.0230374100. PMC 153653. PMID 12679517.{{cite journal}}: CS1 maint: multiple names: authors list (link). Retrieved 2008-08-11. {{cite web}}: Cite has empty unknown parameter: |coauthors= (help); External link in |work= (help); Italic or bold markup not allowed in: |work= (help); templatestyles stripmarker in |work= at position 1 (help)

My suggestion which is very similar to yours is to divide into the following five classes:

• "neurotransmitters" (adrenergics, purinergics, serotonin, etc.)
• peptides
• other hydrophobic "small molecules" including eicosanoids, lipids, steroids
• orphans
• miscellaneous

Does this look reasonable? Boghog (talk) 18:01, 20 April 2010 (UTC)

I am in the process of regrouping the template here. Boghog (talk) 19:02, 20 April 2010 (UTC)

OK, the first draft of the regrouping is finished. How does this look? Please note that I classified the cannabinoid opioid receptors as peptide receptors based on their endogenous ligands. Cheers. Boghog (talk) 19:31, 20 April 2010 (UTC)

Opps, my mistake, moved cannabinoid receptors to small molecule signaling molecule section. Boghog (talk) 04:13, 21 April 2010 (UTC)

After a few more edits, I have gone ahead updated the production version. I hope this version is OK. Of course, feel free to make further adjustments if necessary. Boghog (talk) 20:27, 20 April 2010 (UTC)

Interesting to note that along with GPR55 and GPR119, GPR18 has now also been implicated as a novel cannabinoid / fatty acid amide receptor, meaning we could well have five cannabinoid receptors to deal with! The field just keeps getting more complicated... Meodipt (talk) 04:29, 21 April 2010 (UTC)

Thanks for the heads up. I saw your edits and have added GPR55 and GPR119, GPR18 to the list of cannabinoid receptors in the {{G protein-coupled receptors}} template. Cheers. Boghog (talk) 05:10, 21 April 2010 (UTC)

Updated IUPHAR links responding

~Thanks for the work on these links, we have been rather busy and out of touch of late. But I'm still interested in continuing to encourage pharmacologists to fill in the receptor stubs..... Not easy to recruit volunteers! Another suggestion, we have been slowly curating drugs and other experimental chemical modulators of the IUPHAR-receptor set, each compound now boasts a ligand page (e.g.http://www.iuphar-db.org/DATABASE/LigandDisplayForward?ligandId=34) with some interesting information. It would be nice to link out to your growing list of drugs from each page... Please could we have a list of the wikipedia compound_ids and their SMILES? What is the best way to link to your chemicals?

ever SMILING

--Chidochangu (talk) 16:29, 13 April 2010 (UTC)

Good to hear from you again. Implementing the IUPHAR links was rather straight forward.

I could be wrong, however I do not think anyone has constructed a paired list of SMILES strings vs. Wikipedia drug articles. Wikipedia by its vary nature is very diffuse and unless someone makes a special effort to index a topic such as drug articles vs. SMILES stings, these types of indices are generally not available. Concerning ways of finding wikipedia drug articles to link to, I noticed that aripiprazole IUPHAR entry has CAS and PubChem accession numbers. Given either of these IDs, one can do the following types of searches to located the corresonding Wikipedia article name:

• CASNo = 129722-12-9
• PubChem = 60795

If you can supply me a list of CAS and/or PubChem registry numbers, I can return to you a list of corresponding Wikipedia article names.

On a related topic, would it be possible to link IUPHAR receptor and ion channel entries back to the corresponding Wikipedia Gene Wiki articles?

Cheers. Boghog (talk) 18:53, 13 April 2010 (UTC)

Hi Boghog

Thanks for the quick response, (I see you have not lost your touch, efficient as ever !!!)

I certainly will prepare a list of iuphar_id v. pubchem_id for you (this is do able, i may even run a small script to get the appropriate wikipedia article names myself to save you time). If you want to include IUPHAR_IDs in the list of identifiers e.g. chemspider, drugbank etc you are welcome

As for the IUPHAR receptor to wikipedia links I do not have any problem with.. I will have a look at the best way to incorporate the links onto our pages and get back to you.

cheers ever SMILIN--Chidochangu (talk) 07:30, 14 April 2010 (UTC)

Hi Boghog again.. twice in a day!!

Here is the csv file containing the IUPHAR_IDs VS. PubChem_IDs link: relevant file

please can you provide the list of wikipedia article names?

I will get back to you soon on the iuphar_receptor page to wiki_gene links

eva SMILIN --Chidochangu (talk) 14:04, 14 April 2010 (UTC)

Thanks for assembling the list of CAS registry numbers. Unfortunately these have been corrupted by Excel (if you paste a CAS number into Excel, Excel thinks it is a formula and treats the dashes as minus signs, and substracts the second and third fields from the first and displays the result). Before you paste the registry number into Excel, you need to first change the format of the cells to "text". I would appreciate if you would update you file with non-corrupted CAS numbers. Thanks. Boghog (talk) 04:55, 16 April 2010 (UTC)

Hi Boghog

No these are not corrupt CAS numbers by PubChem..... (I would never serve corrupt CAS to anyone)

Ooops did I not mention that we have provided the iuphar_id vs pubchem_ids not the CAS...see csv file again relevant file. Our list of CAS numbers is not exhaustive and we think it better to use the PubChem ones... I also have InCHIs for all iuphar compounds if this helps any?

We have also identified a good place on our pages to link out to all the genes on wikipedia from our receptor pages please could you send us a list of all the wiki_gene ids vs. iuphar_receptor numbers and we should have it on line by mid-week...

I hope to hear from you soon... there are some noises within IUPHAR about getting the stubby ones updated in a more systematic way... please keep nagging me on this..

I have lost my old password and do not have access to the Phamarcology group...arrrrr

yours with SMILEs InCHIs wide --Chidochangu (talk) 10:07, 16 April 2010 (UTC)

Opps, sorry about that. When I responded, I was very tired and I didn't read your message very carefully. I will supply you the PubChem/Wikipage and wiki_gene ids vs. iuphar_receptor numbers this weekend. Cheers. Boghog (talk) 10:39, 16 April 2010 (UTC)

Hi Chidochangu. Per your request, I have compiled a tab delimited list of IUPHARDB ligand IDs vs Wiki pages. Concerning adding returning links from these Wikipedia articles to the IUPHARDB, again I will ask consensus from the community. I don't think there will be any objection, especially since the IUPHARDB ligand entries will link to Wikipedia pages, but nevertheless I still should ask. Concerning linking to Wikipedia receptor/ion channel pages, for the most part, the pages are named after the HUGO symbol or there is a redirect from the HUGO symbol to the Wikipedia article. I am currently double checking this to make sure (so far I found a few missing redirects which I have now added). More later. Cheers. Boghog (talk) 06:38, 19 April 2010 (UTC)

Hi there Boghog we have implemented drug id links to wikipedia on our test database, however we noticed some errors in the list you sent ( please see a few examples below:)

--iuphar_name, iupharId, pubchem, wikipedia, wiki_PubChem

--bromocriptine, 35,2443,Resveratrol,445154

--bupivacaine,2397,2474,Hydroxy-1,4-benzoquinone,151011

I'm sure how this happened but it appears to come form the list you generated IUPHARDB ::::ligand IDs vs Wiki pages.

Can you help me check this on your end before we go live at IUPHAR-DB?

Thanks again (I would trust SMARTS or SMILES InCHIs to link out )

--Chidochangu (talk) 14:52, 23 April 2010 (UTC)

Sorry for the errors. I have now manually checked and corrected the entire list.

The only way I could figure out how to retrieve these records was to use a perl/google script to search Wikipedia for the PubChemIDs:

#!/usr/bin/perl

use Google::Search;
use strict 'subs';

if ($#ARGV != 1) {
   die("\nUsage: infile outfile\n");
}
    
$file1=shift(@ARGV);
open(INFILE,"${file1}") ||
   die("\nTrouble opening $file1\n");
$file2=shift(@ARGV);
open(OUTFILE,">${file2}") ||
   die("\nTrouble opening ${file2}\n");

while (<INFILE>) {
    chomp;
    my @fields = split(/,/);
    my $index   = $fields[0];
    my $PubChem = $fields[1];
    my $query   = "site:en.wikipedia.org PubChem " . $PubChem . " -user:" ;
    my $search  = Google::Search->Web( q => $query );
    my $result  = $search->first;
    if ($result ne '') {
       my $article = $result->uri;
       print OUTFILE "$index\t$PubChem\t$article\n";    
    }
}

Using Google to search Wikipedia for example "site:en.wikipedia.org PubChem 60795 -user:" usually works, but as you can see from all the errors, not always. I don't know a better way of doing this. Searching for InCHIs might be the best way, but unfortunately most of the Wikipedia ligand articles do not contain InCHIs codes. SMILES is more commonly included, but there are many ways of writing a SMILES string for the same structure, so searching for SMILES will not work (there are ways of canonicalizing SMILES strings so that they are identical no matter what the order of the inputed atoms into the SMILES string generator, but unfortunately there is no universally accepted canonical SMILES algorithm). Boghog (talk) 07:06, 24 April 2010 (UTC)

Hi Boghog,

Thanks for the file we have now implemented the links on our production database.. we will let you know as soon as we go

live online.. the links work. I will try the InCHIs just to check if there is something missing or with multiple pubchems

I noticed pubchem is sometimes notorious for this, esp with chiral compounds...(where the chiral specification is dubious)

Any luck with the issue wikipedia links back to IUPHAR-DB.?? Please could you supply a similar list for the receptors as you did with ligands so I can reciprocate the receptor links from IUPHAR-DB.

Thanks again [EVER SMILIN] --Chidochangu (talk) 16:01, 26 April 2010 (UTC)

Hi Chidochangu. Thanks for the update. The search I did is bound to miss some Wikipedia ligand articles since as you point out, there may be more than one PubChem ID for a given chemical. So searching with InCHIs may indeed locate some addition articles. I am kind of busy right now, but I haven't forgotten about my promise to provide you with a list of (1) Gene Wiki articles that link to the IUPHAR-DB and also (2) linking Wikipedia ligand pages to the IUPHAR ligand DB. I should be able to complete both tasks this weekend. Cheers. Boghog (talk) 19:47, 26 April 2010 (UTC)

Help with Pentapeptide repeat page

Dear Boghog2,

Thanks for your help with the Pentapeptide repeat page images and layout. It looks much better now. You are totally awesome :) Alexbateman (talk) 08:45, 2 May 2010 (UTC)

No problem. I just made a couple of quick adjustments with GraphicConverter (image cropping; jpg → png conversion) . Cheers. Boghog (talk) 10:24, 2 May 2010 (UTC)

IUPHAR link update

Hi Chidochangu,

I have compiled a mapping of Wikipedia receptor/ion channel articles to IUPHAR database entries here. (Please note that many of these are piped redirects. You should link to the page name after the pipe to directly link to the Wikipedia article.) If you could add these links to the IUPHAR database, I would greatly appreciate it. In addition, I have made a request here to add a link from the {{Drugbox}} to the IUPHAR database. Cheers. Boghog (talk) 17:43, 2 May 2010 (UTC)

Hi Boghog,

Thanks for the list, we will add the wiki_gene links from IUPHAR-db soon...! As you may already know IUPHAR-db will be adding a :: set of nuclear hormones to the classes they cover in the summer.. we may have to re-do this again sometime soon.

cheers --Chidochangu (talk) 10:49, 3 May 2010 (UTC)

Thyroxine deiodinase

Hi! I saw you did such a good job with Iodothyronine deiodinase and Iodotyrosine deiodinase entries, you might want to look at a remark I made in the Discussion section of Thyroxine deiodinase. I do not know enough to make the right call, but it seems very likely that you do :) Thank you. -- 83.9.135.174 (talk) 14:06, 3 May 2010 (UTC)

Thanks for the heads up. Per your suggestion, I have merged the contents of the thyroxine deiodinase article into iodothyronine deiodinase and also cleanup slightly the deiodinase article. Cheers. Boghog (talk) 20:21, 3 May 2010 (UTC)

ZM-241,385 wrong structure?

Hi Boghog, Thanks for the request to link out to the IUPHAR ligands, I think this will be beneficial to users! I also think we have an error on wikipedia see [wrong_structure?]. The correct links for this compound can be found on [correct_structure?] see the pubchem_id, cas-number, and chebi_id for this compound on this page. I think the literature you used and the text is correct for the Wikipedia drug page. I hope this is a good example of how we can help each other in the future, as IUPHAR adds new compounds to their database!

--Chidochangu (talk) 10:10, 5 May 2010 (UTC)

Thanks for catching the error. I originally obtained the structure from the PubChem record 5311506 which is in error whereas PubChem 176407 contains the right structure. I have corrected the structure, IUPAC name, and SMILES string in the ZM-241,385 article. Likewise, I think this is a great example of how we can help each other. Cheers. Boghog (talk) 19:15, 6 May 2010 (UTC)

I just noticed that the tritiated ZM-241385 entry in the IUPHAR-DB (see 455) contains the same structural error. Cheers. Boghog (talk) 19:35, 6 May 2010 (UTC)

Ezrin

Hi! I'm really a newbe in wiki, and I edit the ERM protein family entry. I was planning to edit Ezrin entry next...but you've done a great job already!

Thanks for updating this entry! Machicoa (talk) —Preceding undated comment added 20:31, 11 May 2010 (UTC).

And thank you for expanding the ERM protein family article! You have done a great job. Please carry on and if I can be of any assistance, please don't hesitate to ask. Cheers. Boghog (talk) 20:41, 11 May 2010 (UTC)

Pyruvate Carboxylase page

boghog, thanks for editing especially fixing my formatting on Pyruvate carboxylase! I'm (extremely) new to wikipedia and working on a class project. as a head's up i'm looking to expand the mechanism and biological significance sections and probably add a role in anaplerosis section.

Sswilson7 (talk) 16:54, 14 May 2010 (UTC)

Your doing a great job of expanding the pyruvate carboxylase article! It looks like you are catching on very quickly. Let me know if you have any questions and I look forward to your additional contributions to the article. Cheers. Boghog (talk) 18:06, 14 May 2010 (UTC)

Stanford Biochemistry class project

Dear Boghog2,

Thanks so much for working so hard to make Wikipedia's protein and enzyme pages so helpful, accurate, and nicely laid out. You're really doing the community a huge service. My students are editing Wikipedia pages as part of a class project, and are being graded based on their efforts. It will make my work much easier if you could hold up on fixing up their work until after Friday the 21st. Please let me know if this seems reasonable to you. Again, I personally greatly appreciate the effort you've obviously put in to helping out the entire biochemical community.

Best,

Alex Dunn

[email redacted, visible via dif] —Preceding unsigned comment added by 171.66.82.245 (talk) 02:15, 18 May 2010 (UTC)

Great! Your students are adding some excellent content that has greatly improved these articles. I apologize for complicating your grading. Per your request, I will hold off further editing of these enzyme articles until this weekend. I do very much appreciate the high quality contribution that you and your class are making to Wikipedia. Cheers. Boghog (talk) 04:22, 18 May 2010 (UTC)

Forgive my intrusion, but I've redacted the email from the above post, as there are evil robots that crawl the web searching for email addresses their masters can add to spamlists. See address munging for workarounds. Adrian J. Hunter^{(talk•contribs)} 16:16, 18 May 2010 (UTC)

Files

Would you like to receive some computer-generated and partly wikified files from me about protein families (see my recent edits)? Or maybe someone else would? If so, please send me a message through my WP email. Ideally, this should be done by a bot, but I am not really in this business. Great job you are doing! Warm regards. Biophys (talk) 20:41, 25 May 2010 (UTC)

HI and welcome back! And thank you for your kind words. I have missed you.

I would have sent you a private e-mail, but you don't seem to have this activated at the moment. Depending on how much work is involved, I may be interested in systematically creating pfam protein family articles using BogBot. Please send me a few example files. I will take a look and get back to you. In addition, if this project involves creation of more than a few dozen articles, we should ask the community for support before proceeding. I look forward to working with you again. Best regards. Boghog (talk) 06:20, 26 May 2010 (UTC)

Done. Please send me something. I will send you three files and a few comments.Biophys (talk) 13:10, 26 May 2010 (UTC)

It looks like all protein pages should be renamed per Uniprot nomenclature [1]. We need normal names/titles of the articles rather than faceless gene codes (which would remain as redirect pages). What do you think? Biophys (talk) 02:51, 27 May 2010 (UTC)

I agree that in many cases, Gene Wiki pages should be renamed to the recommended UniProt protein name. However some of these UniProt names are quite long. An alternative UniProt name may be preferable if available. There may be a few cases where a concise gene name might be preferable to a verbose protein name. Worse yet, occasionally the translated protein products of different gene have identical UniProt names. In these cases, I think the gene name or symbol is preferable.

Unfortunately I don't think a bot will be able to sort through all these alternative solutions. Each case is unique and requires human common sense to make a decision. I think RADIL is a boarder line case and I don't have a strong feeling whether this article should be renamed to Ras-associating and dilute domain-containing protein or remain RADIL. Boghog (talk) 19:15, 27 May 2010 (UTC)

Agree about the names. I sent you two files. Do not forget placing this template (

This article incorporates text from the public domain Pfam and InterPro: IPR001248

) when using content of the first file. Then it will be properly recognized by Corenbot. The second one was prepared by me, and am giving it under GDFL for free. One might simply download the both files onwiki by treating them as graphic files but transforming them to .PDF. Of course, one should not simply copy-paste the content, but modify it whenever is needed and understand the subject. Cheers, Biophys (talk) 03:30, 28 May 2010 (UTC)

Talkback

Hello, Boghog. You have new messages at Talk:Apoptosis_regulator_proteins,_Bcl-2_family.
Message added 09:48, 6 June 2010 (UTC). You can remove this notice at any time by removing the {{Talkback}} or {{Tb}} template.

Regarding the merger proposal. GiftigerWunsch [TALK] 09:48, 6 June 2010 (UTC)

Centrosome template

Hi Boghog, thanks a lot for expanding the centrosome template and adding the navbox to the proteins pages. I was just wondering if you did this manually or with some sort of script. best, MichaK (talk) 07:39, 7 June 2010 (UTC)

Hi MichaK and thank you for your contributions to centrosome protein pages! The edits I made to the {{centrosome}} template and the articles it links to were all done manually. Unless they are more than a few dozen edits to be made, it is usually not worth the effort to write a bot script. I intend to create articles for the remaining red links in the template once I have a free moment. Cheers. Boghog (talk) 10:44, 7 June 2010 (UTC)

NLR pages

Thank you!!!! -- for making all those protein boxes. I am in your debt!! ~ Ciar ~ _(Talk) 20:24, 14 June 2010 (UTC)

And thank you for creating these articles! In case you are interested, there is a tool here that may be used to create both the protein infobox and article. There are a few bugs and you will need to fix these manually, but nevertheless using this tool is much easier that creating these articles and templates from scratch. Cheers. Boghog (talk) 04:01, 15 June 2010 (UTC)

Oooooh, great! Thanks....I am soooo behind the times!! ~ Ciar ~ _(Talk) 05:18, 15 June 2010 (UTC)

Endorphin

Hi! You reverted on Endorphin but the simplified text is back again. I don't want to revert again, because I have too many reverts there as it is (even though one of the reverts was a revert of my own revert). Maybe you could revert to a previous version? Thank you! Lova Falk talk 18:57, 19 June 2010 (UTC)

OK, I have reverted one more time and added a {{uw-3RR}} template to the editors talk page. Hopefully we can engage the editor in a discussion on the article's talk page. Cheers. Boghog (talk) 21:05, 19 June 2010 (UTC)

Thanks! :) Lova Falk talk 08:26, 20 June 2010 (UTC)

Ribonuclease T1 page

Hey! Thanks for the edits to Ribonuclease T1. Do you have any experience with using images from PDB on Wikipedia? The PDB Policies & References page seems to allow this, but I can't find the right image copyright tag. Eigma (talk) 21:22, 16 June 2010 (UTC)

Opps. Sorry for not responding to your post sooner. I may have missed your post since it was placed at the top rather than the bottom of my talk page. Concerning copyright tags, my suggestion is to use the {{attribution||Protein Data Bank}} template. Boghog (talk) 21:44, 19 June 2010 (UTC)

My mistake, I will have to review talk page etiquette ;) Thanks for making the change to the file description page. Eigma (talk) 02:10, 20 June 2010 (UTC)

COPE

Looks like great resource [2]. However, the author is rather eccentric.Biophys (talk) 20:07, 20 June 2010 (UTC)

Template:Infobox protein family and the PROSITE field

Heya, I've been going through the protein domains and I've come across an inconsistency: the field PROSITE is written in lowercase (Prosite) on a lot of pages. I could go through and correct them all, but that would be a pretty big task. The other option (which I suspect would be a lot easier to achieve) would be to make a change to the template and allow either PROSITE or Prosite as valid options. I know you've put a lot of work into the protein domain pages and have a lot more experience on wikipedia that me, so i was wondering if you might want to help with this little tweak. Ta Abergabe (talk) 12:45, 24 June 2010 (UTC)

And thank you for adding all those images and other fixes to pfam boxes! Per your request, have added the option for the Prosite parameter to be written in "Title case". I have tested the modified template and it seems to work. Please note that articles that already contain the "Prosite" parameter may not immediately display the link. It may take a few days all these pages to be updated. Alternatively you can force an update on individual pages by hitting the edit tab on the article and replace "action=submit" with "action=purge" followed by return in the address window of your web browser. Cheers. Boghog (talk) 13:33, 24 June 2010 (UTC)

Cheers, you're a star ^_^ Abergabe (talk) 13:36, 24 June 2010 (UTC)

Question about Python

Hi! Seeing that your bot is running on Python: Do you know a good way of adding parameters to templates, or of modifying existing ones (like a PyWikipediabot function or some code you have already written)? Just wanted to ask before I start reinventing the wheel. --ἀνυπόδητος (talk) 18:37, 25 June 2010 (UTC)

Hej Anypodetos. The closest thing I did to modifying a template with a python script was to merge and replace the contents of four templates into one new template (see this diff for an example). The Python script that I used for this task may be found here. To find articles that include the template, I used the Wikipedia "what links here" function (for example) and captured the raw html output in the web browser to a file. In my Python script, the "regexp_article.search(line)" was used to parse for the article title. I then looped over these titles. If you want to modify a template, replace the following in my script:

if not ( regexp_er.search(line) or regexp_cas.search(line) or regexp_go.search(line) or regexp_el.search(line) ):

with something like:

if ( regexp_template.search(line) ):

I am far from an expert Python programmer, but the above example worked for me. I hope this helps. Cheers. Boghog (talk) 19:54, 25 June 2010 (UTC)

Thanks a lot! I will have to tweak that a bit for my purpose, but it's an excellent starting point. And in case you didn't know: the function ReferringPageGenerator in pagegenerators.py produces the same list of pages as the "what links here" function. Cheers, ἀνυπόδητος (talk) 10:55, 26 June 2010 (UTC)

Defensins

Dear BogHog2,

Thank you for your message, and please forgive my uninitiated editing. I should have left existing pages alone. My main objective is to complete the set of human alpha defensin pages, and to make redirect pages so that the many synonyms all point to well-referenced pages named after each defensin protein or gene. The style of antimicrobial peptide pages should be as similar as possible to entries of other proteins such as enzymes. However, defensins aren't enzymes. Perhaps antimicrobial peptides should be treated a little differently than enzymes.

My objection to the language "in humans" in the leading sentence defining each defensin gene is the implication of standardization of gene names across more than one species, which isn't the case. For example, DEFA1 encodes human alpha defensin 1--human only. Mouse alpha defensin 1 is far less similar to DEFA1 than it is to other mouse defensins.

Best regards,

Bcericksen (talk) 13:20, 15 June 2010 (UTC)

Opps. Sorry about that. I now see that the defensin nomenclature is far more complicated than I thought. I was under the impression that the gene names for most proteins (enzyme or not) were standardized across species, as for example, can been seen in the HomoloGene entries for the estrogen receptor isoforms:

• ER-α
• ER-β

In agreement to what you wrote above, the HomoloGene entries for alpha defensins show much less consistency in their nomenclature:

HomoloGene:121760

• DEFA1 Homo sapiens
• DEFA1B Homo sapiens
• DEFA3 Homo sapiens

HomoloGene:123099

• DEFA1 Pan troglodytes

HomoloGene:48059

• DEFA4 Homo sapiens
• DEFA4 Pan troglodytes

HomoloGene:88502

• DEFA5 Homo sapiens
• DEFA5 Pan troglodytes

not listed in HomoloGene:

• DEFA6 Homo sapiens

So it appears that the articles for alpha defensins need to be handled differently from most other Gene Wiki pages. Based on the HomoloGene clustering, it would appear that DEFA1, DEFA3, and DEFA6 are uniquely human whereas for DEFA4 and DEFA5 there is at least one ortholog with the same name. So as a compromise, I suggest that the DEFA1, DEFA3, and DEFA6 articles specify that these are human genes whereas with DEFA4 and DEFA5, we could keep the "that in humans" phrasing of the lead sentence. Does this sound reasonable? Regards, Boghog (talk) 20:29, 15 June 2010 (UTC)

There are defensins A1 and A3 from other species [3], [4]. Nothing special.Biophys (talk) 02:52, 16 June 2010 (UTC)

I think you have missed the point. Human DEFA1 is more closely related to human DEFA3 than it is to mouse Defa1. Gene duplication occurred after speciation for many of the alpha defensins and the currently used nomenclature for these genes has not taken this into account (see figure 3 in PMID 15494476; in the figure human DEFA1 = primate DEFA1/2, mouse Defa1 = mouse Defcr1, these two gene are in completely different clusters). Boghog (talk) 09:28, 16 June 2010 (UTC)

Right. Duplication after speciation. This should happen all the time, messing up orthology relations. There are should be many other examples.Biophys (talk) 22:07, 16 June 2010 (UTC)

For what it is worth, a blast search through the mouse protein database using the protein sequence of human DEFA1 produces in decreasing order of similarity alpha-defensins 20, 11, 5, 14, 10, 24, 6/12, 16, 4, 7, 23, 5, and finally 1. So it is misleading to say mouse Defa1 is a homolog of human DEFA1. It is perhaps more accurate to say that the mouse alpha-defensin gene family are orthologs of the human alpha-defensin family. Boghog (talk) 04:23, 17 June 2010 (UTC)

Here in Figure 1 are separate alignments of the mouse, macaque, guinea pig, rabbit and rat defensins, showing that defensins are numbered within each species, independent of the numbering schemes of other species. Bcericksen (talk) 02:08, 15 July 2010 (UTC)

It's also insightful to look at the disparate names chosen by UniProt. Searching for human alpha defensin 1 returns many defensin genes. Human alpha defensin 1, which I would call HNP1 (Human Neutrophil Defensin 1), is encoded by the DEFA1 gene and named "Neutrophil Defensin 1" in the UniProt database. Human alpha defensin 2, or HNP2, is absent from the list, presumably because it is a post-translational modification of the DEFA1 gene product. Human alpha defensin 3, or HNP3, is named "Neutrophil Defensin 3" by UniProt. Similarly, human alpha defensin 4, or HNP4, is named "Neutrophil Defensin 4" by UniProt. However, Human Alpha Defensins 5 and 6, which I would call HD5 and HD6, are expressed in Paneth cells, not the neutrophil. UniProt omits the cell type and adds hyphens: "Defensin-5" and "Defensin-6". The names most commonly used in the defensin literature (HNP1, HNP2, HNP3, HNP4, HD5, and HD6) are not shown as search results, but they do appear as alternate names in each UniProt entry. The complex nomenclature is best addressed by listing the major synonyms in the first sentence of each Wikipedia page.

Changing the phrase "in humans" to the adjective "human" has made the first sentence much clearer. I would further suggest that it should be supplemented with the synonym, "Human alpha defensin 1", wherein "alpha defensin" links the the alpha defensin entry that shows all six amino acid sequences. Other defensin pages, for example Beta-defensin 2, could also benefit from changes along these same lines. Bcericksen (talk) 02:06, 15 July 2010 (UTC)

I have further modified the lead sentences of DEFA1, DEFA3, and DEFA6 per your suggestions. However per WP:BOLDTITLE, I did not include a link to alpha defensin within the bolded term, but rather included the link in the next sentence. I will take a look at the beta definsin articles when I find time. Please feel free to go ahead and modify these yourself. Cheers. Boghog (talk) 07:48, 15 July 2010 (UTC)

Further reading section

Hi,

I saw that you have been editing Colipase. I really like the further reading sections. In fact I added one last week to the GcvB RNA article. But I did that manually by searching pubmed and then cutting and pasting each pubmed id into the online template filler. It was pretty tedious to do. But it was super useful for the expansion of that article that I have underway. I'd quite like to do this for some other non-coding RNA articles so if you have a less manually intensive approach I'd love to hear about it. Alexbateman (talk) 21:48, 13 July 2010 (UTC)

In the particular example of colipase, I used the GeneWikiGenerator. That probably is not going to do you a lot of good with non-coding RNA articles. If you already have a list of PMIDs, there are at least two scripting alternatives. The first is David Iberri's perl source code. The documentation is a bit cryptic, so below is a simple script that might be helpful in getting you started. The example will create a citation template for PMID 8566796:

#!/usr/bin/perl
use WWW::Wikipedia::TemplateFiller;
my $filler = new WWW::Wikipedia::TemplateFiller();
my $source = $filler->get( pubmed_id => '8566796' )->fill;
my $string = $source->output( add_ref_tag => 1, 
  vertical => 0, 
  add_accessdate => 0, 
  dont_use_etal => 1, 
  omit_url_if_doi_filled => 1, 
  extended => 0, 
  add_param_space => 1 );

print "$string\n";

The following is a Python scripting solution:

#!/usr/bin/python

import re
import string

from Bio import Entrez
from Bio import Medline

Entrez.email = "your_email@domain.com"

months = {'01': "Jan", '02': "Feb", '03': "Mar", '04': "Apr", '05': "May", '06': "Jun", '07': "Jul", '08': "Aug", '09': "Sep", '10': "Oct", '11': "Nov", '12': "Dec"}

def PubMed_Citation(PubMed_ID):

  handle = Entrez.efetch(db="pubmed",id=PubMed_ID,rettype="medline",retmode="text")

  records = Medline.parse(handle)

  ref = ""
 
  for record in records:

	if record.has_key("AU"):
	  author_list = ""
	  for author in record["AU"]:
		author_list = author_list + ", " + author
	  author_list = author_list[2:]
	else:
	  author_list = ""
  
	if record.has_key("TI"):
	  title = record["TI"]
	  if (title[-1:] == "."):
	    title = title[:-1]
	else:
	  title = ""
	  
	if  record.has_key("TA"):
	  journal = record["TA"]
	else:
	  journal = ""
  
	if record.has_key("VI"):
	  volume = record["VI"]
	else:
	  volume = ""
  
	if record.has_key("IP"):
	  issue = record["IP"]
	else:
	  issue = ""
	
	if record.has_key("PG"):
	  pages = record["PG"]
	else:
	  pages = ""
	
	if record.has_key("DA"):
	  year = record["DA"][:4]
	  month = months[record["DA"][4:6]]
	else:
	  year = ""
	  month = ""
	
	if record.has_key("PMID"):
	  pmid = record["PMID"]
	else:
	  pmid = ""
	  
	if record.has_key("PMC"):
	  pmc = record["PMC"][3:]
	else:
	  pmc = ""
	
	if record.has_key("AID"):
	  doi = ""
	  for item in record["AID"]:
	    elements =item.split(" ")
	    if (len(elements) == 2):
	      if elements[1] == "[doi]":
	        doi = elements[0]
	else:
	  doi = ""
	  
	ref = ref + "<ref name=\"pmid" + record["PMID"] + "\">{{cite journal | author = " + author_list + " | title = " + title + " | journal = " + journal + " | volume = " + volume + " | issue = " + issue + " | pages = " + pages + " | year = " + year + " | month = " + month + " | pmid = " + pmid  + " | pmc = " + pmc + " | doi = " + doi + " }}</ref>"
  
  return ref

I hope that you find at least one of these suggestions useful. Cheers. Boghog (talk) 20:25, 14 July 2010 (UTC)

Thanks! I'll use the perl code as a starter. Alexbateman (talk) 21:13, 14 July 2010 (UTC)

Category

What do you think about this: [5]? Biophys (talk) 22:02, 21 July 2010 (UTC)

User:ProteinBoxBot/Requests

<16 minutes! Not bad. Many thanks. --Paul (talk) 20:34, 31 July 2010 (UTC)

Your welcome. Just a coincidence that I happened to be on-line when you made the request, so I was able to quickly act on it. Cheers. Boghog (talk) 21:16, 2 August 2010 (UTC)

TCACycle template

I've moved {{TCACycle WP78 offset}} for you so that "Template:" isn't repeated twice. —Jeremy ^{(v^_^v Carl Johnson)} 21:10, 2 August 2010 (UTC)

An obvious case of copy and paste without carefully checking the template name I created. Thanks for catching that. Cheers. Boghog (talk) 21:14, 2 August 2010 (UTC)

Null perspiration, chummer. The redirect is still in place; I can tag it for speedy deletion (as an implausible redirect) if you wish. —Jeremy ^{(v^_^v Carl Johnson)} 21:15, 2 August 2010 (UTC)

Template on CFL2 (gene)

Hi, this [6] has left a broken template '"{{PDB Gallery|genei' on CFL2 (gene). Can't fix it by myself as I have absolutely no clue about genetics. Found the error on [7]. Thanks --Ben Ben (talk) 15:04, 4 August 2010 (UTC)

Thanks for catching the error. There is only one structure that has been determined for this protein to date, so transcluding the PBB gallery template ({{PDB Gallery/1073}}) into this article would be redundant (the graphic is already included in the protein infobox). I have therefore completely removed the template. Cheers. Boghog (talk) 15:19, 4 August 2010 (UTC)

BTRC (gene)

Heya, i'm just wondering about the opening line; would be better to put the gene as the focus of the article:

The '''BTRC''' (beta-transducin repeat containing) '''gene''' in humans encodes for the protein F-box/WD repeat-containing protein 1A, also known as '''pIkappaBalpha-E3 receptor subunit'''.

Than the protein it encodes for:

The '''F-box/WD repeat-containing protein 1A''' also known as '''pIkappaBalpha-E3 receptor subunit''' is a [[protein]] that in humans is encoded by the ''BTRC'' (beta-transducin repeat containing) [[gene]].

Hi! Concering the lead sentence in Gene Wiki articles, as discussed here and here, we have tried to make clear that these articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:

• <recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.

The "that" in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human. Since much of the text in this particular article focuses on the properties of the protein (structure, function, interactions with other proteins), I think it is appropriate that emphasis in the lead is on the protein. Does this sound reasonable?

PS: your doing a great job of cleaning up and expanding a lot of pfam, protein, and enzyme pages. Keep up the good work! Cheers. Boghog (talk) 20:27, 18 August 2010 (UTC)

Ahh cool, I'm with you now :) And cheers, it's been great fun ^_^ Abergabe (talk) 08:43, 19 August 2010 (UTC)

Infobox_rfam

Dear wise, glorious and noble Boghog, I have been doing a bit of work on the SMK_box_riboswitch page. This riboswitch has a number of pdb structures but the Infobox_rfam doesn't seem to work in quite the same way as Infobox protein family. Do you have any hints on how I should deal with this?--Paul (talk) 22:17, 25 August 2010 (UTC)

I must admit that I don't completely understand the template syntax myself. The {{Infobox rfam}} template was based on the {{Infobox protein}}. The later has the same problem with PDB links as the former. I then modified the {{Infobox rfam}} based on the {{Infobox protein family}} template and the PDB links now seem to work. Cheers. Boghog (talk) 22:47, 25 August 2010 (UTC)

You're a star. Many thanks. --Paul (talk) 07:07, 26 August 2010 (UTC)

DYK query

Could you check Template_talk:Did_you_know#Protein pigeon homolog? Thanks Smartse (talk) 16:34, 2 September 2010 (UTC)

DYK for Protein pigeon homolog

Materialscientist (talk) 07:19, 11 September 2010 (UTC)

Pharmacokinetic_parameters.png at Commons

Hi! Can you please fix a little error? The shaded area (AUC) should stretch down to y=0 (not only to C_min). →Alfie±Talk 14:32, 13 September 2010 (UTC)

Edit: Is there any reason why you have chosen four samples within ~7–8 hours? Such a schedule is rather unusual. For a one-compartment drug quite often a geometric progression after t_max is used. The algorithm is: t_i = t_i-1 × (t_n/t₁)^1/(n-1) where i index of the respective time points (2, 3, ..., n), n number of time points, t_i calculated time point at i, t_i-1 previous time point, t₁ first time point, and t_n last time point. →Alfie±Talk 15:22, 13 September 2010 (UTC)

Hi. Thanks for your comments. I realize that the shaded area should stretch down to y=0. The reason it didn't was it was difficult to draw the shading down to the y-axis with the software I was using. I will take another look at this and see if I can fix it. I will also try redraw the curves based on your formula. I am not a pharmacologist, so I may come back to you with a few questions concerning the curve. I am a bit busy at the moment, so it may be a few days before I will have time to work on this. Cheers. Boghog (talk) 21:23, 13 September 2010 (UTC)

Hi! No problem, take your time. Alfie↑↓© 23:19, 13 September 2010 (UTC)

Protein C

Boghog2, I'd really appreciate it if you would stop reformatting Protein C to fit your aesthetic. I'm working very heavily on this article, and every time you make a change, it makes my work significantly harder. I don't see any benefit to your modifications (except the wikilinking, which has been useful), and I assure you there are reasons for my conventions. If you have a suggestion, please suggest it on the talk page, where we can discuss which way works better. In the mean time, please don't make changes that have no effect except to make my editing more difficult. The article is not done, and if I'm the one currently adding material, I need to be able to read the syntax. -- Rmrfstar (talk) 16:36, 13 September 2010 (UTC)

Replied here. Boghog (talk) 21:13, 13 September 2010 (UTC)

NFkB / 1svc

Hi there Boghog2, I was making PNG images from PyMol for a class and came across your upload for NFkB. Your rendering looks nice, but I think you cited the wrong PDB ID. The image you rendered was actually 3d07 (NFkB p100/RelB/DNA) rather than 1svc (NFkB p50/DNA). As my homework is due tomorrow, it would be a great help if you could update the PDB ID before 22-Sept-2010, 8am, since I've already rendered an image of 1svc. Thank you! NguyenJB (talk) 20:43, 21 September 2010 (UTC)NguyenJB

Hi NguyenJB. Thanks for your complement. The release date of PDB: 3DO7​ was on 2009-07-21 and I created File:1SVC.png on 2007-10-3, almost two years before the 3DO7 coordinates were released. So it is impossible that the 1SVC.png graphic could have been made from the 3DO7 coordinates. I also checked through my files on my Mac and I still have the the 1SVC.pdb coordinate, 1SVC.pml pymol script, and 1SVC.png graphics file, all dated 2007-10-3 so I am fairly certain that the graphic depicts the 1SVC coordinates. What precisely about the 1SVC.png graphic doesn't look right? Cheers. Boghog (talk) 21:01, 21 September 2010 (UTC)

Hi Boghog2. I just spent the last hour checking the release dates as well, and I apologize for the misunderstanding. I think I figured out why my rendering looks different from yours -- you were astute enough to find the correct symmetry mate and generate a homodimer, while I just showed the p50 monomer. Do you think there is a place for me on the website to deposit the new ternary complex? NguyenJB (talk) 21:28, 21 September 2010 (UTC)NguyenJB

OK, now I see what the problem is. The coordinates for the full dimer are in the PDB: 1SVC​ file, but the monomers are put in different "states". When you read this PDB file into PyMOL, by default, you only see one monomer at a time. To see both simultaneously, you need to submit the command "set all_states, on" (see all states). Boghog (talk) 21:35, 21 September 2010 (UTC)

Right. Thank you for the suggestion. I just displayed all symmetry mates within 4 angstrom and selected the one that completed the DNA structure, and I think that should work fine due to the inherent symmetry in the space group. Have you taken a look at the ternary complex that was deposited 2009-07-21? The structure looks very similar (which explains why I was initially confused by your rendering) and the sequence of RelB and NFkB p50 are ~41% identical. Since you've spent some time editing this page and presumably know some molecular science, would you mind critiquing my recent upload (http://en.wikipedia.org/wiki/NF-κB#Activation) to the NF-kB page? NguyenJB (talk) 22:40, 21 September 2010 (UTC)

Nice job. I hope you don't mind, but I made a minor copyedit to your figure caption and tracked down the primary citation for this crystal structure (it wasn't listed included in the PDB: 3DO7​ entry but I was able to find it by searching PubMed). Concerning how I created the File:1SVC.png graphic, in looking back at my PyMOL script, I used the "symexp dup" command. Boghog (talk) 16:05, 22 September 2010 (UTC)

PLX4032

Hi Boghog2. Are you sure the structure for this compound is correct? this link shows a related but different structure for the compound, although the one on the page has a pubchem hit which the other one doesn't... Meodipt (talk) 13:32, 22 September 2010 (UTC)

Hi Meodipt. Yes, there was some confusion about the structure (for example see the previous versions of File:PLX4032 BRAF inhibitor.png). But I am 100% certain that the currently displayed structure is correct (see Nature supplementary material). Cheers. Boghog (talk) 13:40, 22 September 2010 (UTC)

See also PDB: 3OG7​ (PDB Ligand Summary for 032 in 3OG7 ). Boghog (talk) 13:51, 22 September 2010 (UTC)

WP:USURP#Boghog

^ Any progress on getting the commons ducks in a row? –xeno^talk 15:40, 24 September 2010 (UTC)

I just put in a request here. Sorry for the delay. Boghog (talk) 21:06, 24 September 2010 (UTC)

SUL for de.wikipedia.org

Hello, I confirm that I'd like to usurp de:User:Boghog. Thank you. Boghog (talk) 20:04, 25 September 2010 (UTC)

SALL

Can you read thoughts [8] [9] or have you just seen my edits to SALL1 and 4? By the way, congratulations to your new name! Is there a baptizing party? --ἀνυπόδητος (talk) 11:22, 26 September 2010 (UTC)

Hi Anypodetos. I routinely look for recent changes in Gene Wiki articles and I noticed your edits to SALL1 and SALL4. I then noticed that these are transcription factors (an old hobby of mine) that needed to be added to the {{transcription factors}} NavBox. Was there any reason that you were interested in these proteins or are they something you ran across by random?

My new name of course is just a simplified version of my old handle. I wanted the simplified name from the beginning but was blocked from doing so since someone else had already taken it. Fortunately they had not made any edits so I was able to usurp the name. It bugged me for a long time, but I just got around to requesting a name change. Not a big deal really. Cheers. Boghog (talk) 11:40, 26 September 2010 (UTC)

I came across Townes–Brocks syndrome (which links to SALL1) by accident. When I come across a gene/protein article without a navbox, I usually try to find an appropriate one or else create one. Only this time I was interrupted, and when I came back, the work had already been done... Cheers --ἀνυπόδητος (talk) 11:59, 26 September 2010 (UTC)

Thank you

I never knew that, thank you for correcting my "correction". - 2/0 (cont.) 17:26, 3 October 2010 (UTC)

And thank you for pointing out what might not be obvious to the average reader. Your edit prompted me to add the wiki link. Cheers. Boghog (talk) 20:22, 3 October 2010 (UTC)

Should ABCC2 be renamed?

Thanks for helping out with the ABCC2 article. I am busy with other stuff which, sadly, leaves me little time for OAT1 and ABCC2. I recommend that the ABCC2 article be renamed "multidrug resistance-associated protein 2". Now that we know what the MRP2 protein does, it is receiving more attention than the gene.

Googling Canalicular multispecific organic anion transporter 1 generates about 3,400 hits.

Googling ABCC2 generates about 4,700 hits.

Googling MRP2 generates about 14,500 hits and

googling multidrug resistance-associated protein 2 generates about 22,000 hits.

KBlott (talk) 16:02, 7 October 2010 (UTC)

As long as the protein name is relatively concise, I have no objection to renaming the article after the protein. The name "multidrug resistance-associated protein 2" is relatively concise, so please go ahead and move the page. BTW, I appreciate all the work you are putting into these transporter articles. Your doing a great job! Cheers. Boghog (talk) 04:59, 8 October 2010 (UTC)

Done. Thanks. I wish I had the time to do the articles justice. KBlott (talk) 23:02, 8 October 2010 (UTC)

How do I convert png files to svg files?

Hi Boghog: I have added the molecular structures of some known MRP2 inhibitors to the ABCC2 page. All of the image files (so far) are svg type except for one, which is png type. The svg images have a light blue background while the png image has a white background. Do you know how to convert the png file to an svg file? KBlott (talk) 00:53, 8 October 2010 (UTC)

Unfortunately I don't think there is a way to convert a png graphics file (bit mapped) into svg (vector) format. One must instead export the file directly from the chemical drawing software in a vector format (e.g., postscript of pdf) and then convert the vector file into svg format. Depending on which chemical structure drawing program and computer operating system you are using, there a couple of options for doing this (see WP:Manual of Style (chemistry)/Structure drawing). I tried several of these methods, but I often had trouble producing good quality svg files (e.g., element symbols were often displaced from the vertices of bonds). Hence I have largely given up creating svg images until a more robust method for creating these can be found. Please note that there is no absolute requirement that chemical structure graphics must be stored in svg format. I think image quality is more important than what format it is stored in. Boghog (talk) 05:15, 8 October 2010 (UTC)

There are already SVGs on Commons. I took the liberty to replace the PNGs. Cheers, ἀνυπόδητος (talk) 09:23, 8 October 2010 (UTC)

Thanks for tracking down the SVGs and updating the article. Cheers. Boghog (talk) 18:27, 8 October 2010 (UTC)

Ditto from me. The table looks much cleaner now. Thank you both for the help. KBlott (talk) 23:07, 8 October 2010 (UTC)

Glycoside hydrolases

Hi Boghog. I resumed some activity and created this page: [10]. Any comments or help would be very welcome.Biophys (talk) 19:27, 9 October 2010 (UTC)

Glad to see that you are actively contributing again. As you point out on Talk:Glycoside_hydrolase_families, the main area that needs attention is adding wiki links to enzyme articles. I will add these as I find time. Cheers. Boghog (talk) 20:17, 9 October 2010 (UTC)

Thank you! Note that I made links to CAZYpedia [11] from each family.Biophys (talk) 01:26, 10 October 2010 (UTC)

File:CGP 52608.png missing description details

Dear uploader: The media file you uploaded as File:CGP 52608.png is missing a description and/or other details on its image description page. If possible, please add this information. This will help other editors to make better use of the image, and it will be more informative for readers.

If the information is not provided, the image may eventually be proposed for deletion, a situation which is not desirable, and which can easily be avoided.

If you have any questions please see Help:Image page. Thank you. --ARTEST4ECHO ^{(talk | contribs)} 17:39, 11 October 2010 (UTC)

Agomelatine

Hi. I see that you are active in the pharma project. (I know virtually nothing about it.) Do you think agomelatine should be pared down by someone who knows what s/he is doing? The project has it listed as Start class. IMO it is just too much. Thanks, Hordaland (talk) 10:47, 5 November 2010 (UTC)

Thanks for the note. Per WP:MEDMOS, I agree that the agomelatine article contains too much experimental detail, especially in the pharmacodynamic and clinical studies sections. I will see what I can do when I get a chance. Cheers. Boghog (talk) 10:58, 5 November 2010 (UTC)

ATP Citrate Lyase

Yes this is for an assignment. I put that info in there because it is one of the options for the guidelines on the project. It is due on Monday so if you want to delete info after December 17th 2010 you can (this will give her enough time to see what I did to the page). I just want to make sure I hit the guidelines and get a good grade. Thanks for the help. jviess —Preceding unsigned comment added by Jviess14 (talk • contribs) 23:39, 20 November 2010 (UTC)

Thanks for explanation about your project. I will hold off on any further editing of these articles until after Monday. However I think the guidelines for your project need to change and therefore I would really appreciate if you would ask your instructor would contact me. Thanks. Boghog (talk) 23:47, 20 November 2010 (UTC)

Thanks!

Spaghettimonster (talk) 21:24, 26 November 2010 (UTC)

Thanks

I just wanted to say thanks for the advice with the Hepcidin and how to use Wikipedia a little bit better. This is the first time I've had to do this for a class to wikipedia and I always knew it could be edited, but never knew how. Once again, thanks for the advice hopefully the shortcuts will help next time I have to do this for Biochemistry and I'm not sure if I am writing to you the correct way, but it's worth a shot! Duossm49 —Preceding unsigned comment added by Duossm49 (talk • contribs) 07:30, 30 November 2010 (UTC)

Thymosin alpha 1 versus prothymosin

Hi Boghog

It makes sense to have separate entries for thymosin alpha and the beta thymosins (as split out by Arcadian). I've tried to improve some of the wording necessitated by the split, but am not yet happy with it. (Problem of historic versus contemporary usage).

Also good to bring together the otherwise separate references to prothymosin alpha. Thanks for that! However, virtually all the "extra reading" now listed under thymosin alpha1 is actually about prothymosin, which has function/properties besides those of its alpha1 fragment. A separate entry for prothymosin alpha would be a good fix, but this is a daunting prospect given that its conserved function is mysterious. Jgedwards (talk) 16:30, 30 November 2010 (UTC)

Hi Jgedwards. My apologizes. I didn't realize that prothymosin alpha may functions separate from thymosin α1. However given that (1) they are both derived from the same PTMA gene, (2) thymosin α1 (according to UniProt UniProt: P06454) is the only cleavage product of prothymosin alpha that has been characterized, and (3) as you point out, not much is known about the function of prothymosin alpha, I think it makes sense to have one article about both peptides. Of course, it must be made clear that these are distinct peptides and one way to do that is to have separate sections on each peptide within the same article. If at a later date the function of prothymosin alpha becomes clearer, then it may make sense to split the articles. Does this sound reasonable? Boghog (talk) 21:05, 30 November 2010 (UTC)

Hi Boghog

No call to apologise! Separate sections within single article, at least for time being, sounds fine. Meanwhile a group at Harvard may have found the holy grail re beta thymosins: a candidate cell surface receptor (Kd 12 nm) and a putative signalling pathway. PMID: 21106936 Gives me a lot else to think about! Jgedwards (talk) 01:41, 1 December 2010 (UTC)

Uterine serpin

Thanks for all the edits and advice. I appreciate it.

One question though - SERPINA14 is on bovine chromosome 21 but does not exist in human. Therefore, should it be listed in the chromosome 21 category or be listed as chromosome 21 in the protein table?Ufpete (talk) 02:00, 2 December 2010 (UTC)Ufpete (talk) 01:55, 2 December 2010 (UTC)

I created a special {{infobox nonhuman protein}} template based on the {{infobox protein}} template so that the chromosome link in the protein box now takes you to bovine (or other organism as appropriate) instead of the human gene. Also, thanks for pointing out the problem with the chromosome category. This was automatically added by the template, but since this new template is for non-human genes, this is clearly no longer appropriate. I have edited the template to remove the category so that the category will no longer automatically be added articles transcluding this template. Boghog (talk) 02:15, 2 December 2010 (UTC)

Enzyme pages

Hey since im new at this sort of thing, i was wondering if you could walk me through the rationalle for some of the updates you made on the glycogen synthase and ppp1r3c pages. Some proper use feedback would be great. If easier feel free to email me, "dave dot bridges at gmail dot com" Davebridges (talk) 17:26, 8 December 2010 (UTC)

Hi. Thanks for your note and for your great contributions! The short answer to your question is that I was following up your contributions with some minor housekeeping edits. Concerning glycogen synthase, my edits were simply to provide a link to the newly created protein phosphatase 1 article and to remove WP:OVERLINKs (normally only the fist occurrence of a term should be linked). My edits to PPP1R3C are somewhat more involved and mostly fall in the category of "while I am at it, I might as well fix a few other things". My edits were again to remove over linking and to convert red to blue links where possible. Completely unrelated to your edits, I also removed some obsolete wiki code per this discussion. Finally, if you have the time and inclination, I would be most grateful if you would expand PP1 which I know very little about. Cheers. Boghog (talk) 19:07, 8 December 2010 (UTC)

re: PP1 should be no problem, Ill take a look at that page plus see if i can add anything to PP2A while I'm at it Davebridges (talk) —Preceding undated comment added 02:33, 10 December 2010 (UTC).

DYK for Kunitz domain

The DYK project (nominate) 12:03, 11 December 2010 (UTC)

Hello again;

Just a quick note of Thanks for the 'removal of those "tortured analogies" '. ~ Betaclamp (talk) 06:54, 23 November 2010 (UTC)

I apologize if you think I was being overly harsh in my edit summary. The reason I removed the analogy is that Wikipedia articles should simply state facts. The problem with analogies is that they are frequently culture or knowledge specific. Not everyone may be familiar with fuel injectors. If one uses an analogy to explain something, one also needs to explain the analog. This make the article unnecessarily complex. Cheers. Boghog (talk) 11:03, 26 November 2010 (UTC)

When I said Thanks I really meant it, no sarcasm this time! I'm glad that you could recognize the effect that they had on me/us.

While there is little time now for me to really scour your messages, I just have time to say that whereas my thorough article betaclamp (with no extraneous material) is based upon passages found in a major book, the term Dna-clamp appears to be merely a misnomer. Can we recruit a specialist for this point? Much obliged. ~ Betaclamp (talk) 07:57, 12 December 2010 (UTC) P.S. my non-contestation is an artifact of 'being new and not wanting to 'step-on-another's-toes' ". May I suggest that you put on your safety shoes?

P.P.S. I do feel the need to placate my 'hack' comment, this will be done by my explanation of why I said it.

'ts about time

I'm delighted to say we have to talk; for now I am working on the supposition that there is no such thing as a Dna clamp that is not also a beta-clamp and I'm working towards proving this. Until then I'll expect Beta clamp to be treated as a separate Article, unless you have another opinion! Merci!

As well, my original 1,000 word beta clamp article contained NO extraneous material. ~ Betaclamp (talk) 07:47, 9 December 2010 (UTC)

Thank you for responding. I have already expressed my opinion here. You wrote above there is no such thing as a Dna clamp that is not also a beta-clamp. Your statement would seem to indicate that you also support the merger, but need time to verify the statement. Or have I misinterpreted what you wrote? Boghog (talk) 07:54, 9 December 2010 (UTC)

My 1000 beneficient words trashed by an unidentified, and by my accounting, a possible hack, NO I never supported any part of the merge after it occurred. Now, you Know that I am still working on your material to work on . . .

...just make sure you do not refer to another editor as a "hack" as you did above, blocks for commenting on the editor, not the edits are known to spontaneously occur (talk→ BWilkins ←track) 10:26, 9 December 2010 (UTC)

OK, now I understand that you did not support the merger. There are two interrelated yet distinct issue here. The first is whether the two articles should be kept separate or merged. The second is the content of these articles. The subject matter of the parent DNA clamp article covers both the dimeric prokaryotic and trimeric eukaryotic protein complexes. Since the parent article is still fairly short and the subject matter of the two articles largely overlap, it makes sense to merge the two articles. If the article grows significantly in size, it may at that time make sense to split the article into two, but for the time being, I think it is better to merge the articles together. Concerning the content, the edits that you are referring to were in my opinion on the whole very helpful, but perhaps not enough effort was made to capture all the information contained in the immediately proceeding version of the article.

I have taken the liberty of restoring the immediately preceding version of the beta clamp article in your user space (see User:Betaclamp/Sandbox). As a way forward, I suggest that you edit this version and let me know when you are finished. We can then decide if the content needs further editing and agree on a suitable article to include this text. Does this sound reasonable? Cheers. Boghog (talk) 21:45, 9 December 2010 (UTC)

Dna-clamp does not contain the info in Betaclamp. It mentions only prokaryotes and condenses my elucidation of the Greek alphabet into a string of gibberish. 1,000 words diminished to 100 cannot be positive. Time is all that stops me from more elucidation! ~ Betaclamp (talk) 08:35, 12 December 2010 (UTC) Except for this: I told Adrian that the 'one thing' from the merge that I loved was the addition of the trimer pictograph that he told me that you inserted. Please do the same for the version that you just reinstated, please. Now I can explain the delay that I've mentioned: at the end of the six pages that I took beta-clamp from there is a short section on PCNA, the label on your trimer pictograph; I've yet to study this, it could be that PCNA is a betaclamp.

The current beta clamp subsection of the DNA clamp does contain a condensed version of the previous beta clamp article. The current version of the DNA clamp also contains graphics of both the dimeric prokaryotic and trimeric eukaryotic enzymes. Again, my suggestion is that you edit the draft version contained in your user space (see User:Betaclamp/Sandbox). After reviewing it, we can then decide if it best to add this material to the DNA clamp article, create a new beta clamp article, or possibly add it to the dnaN article. Does this sound reasonable? Boghog (talk) 09:16, 12 December 2010 (UTC)

Yes it does. The eight or so points made lately by myself are all tied together; I've a few unanswered questions that I'll need to prioritize before making another submission. Meanwhile, would you like me to continue here or would a New Section be preferable? ~ Betaclamp (talk) 06:34, 13 December 2010 (UTC)

Great! A good place to continue this discussion would be here. Cheers. Boghog (talk) 20:40, 13 December 2010 (UTC)

Happy holidays!

Wishing you a merry Winter Solstice, in whatever form you choose to celebrate it, and all the best for 2011! ἀνυπόδητος (talk) 16:23, 24 December 2010 (UTC) Design partly stolen from Fv.

And thank you for helping to make Wikipedia a worthwhile place to collaborate! Best wishes. Boghog (talk) 16:38, 24 December 2010 (UTC)

Happy Holidays!

Seasons greetings and best wishes for 2011! Biophys (talk) 01:35, 25 December 2010 (UTC)

Thanks! I noticed that you took this picture yourself. Cool! Boghog (talk) 19:17, 25 December 2010 (UTC)

Talkback

Hello, Boghog. You have new messages at [[User talk:Ronhjones# · → • ?|Ronhjones's talk page]].
Message added 22:57, 30 December 2010 (UTC). You can remove this notice at any time by removing the {{Talkback}} or {{Tb}} template.