I really think this article needs pretty much entirely rewritten to remain a FA. There is just too much wrong with it, imo, to improve it. I keep looking at it, and I just don't see it improving much in its basic form. I will be glad to review it over the days and add comments if you have time to repair it, but I don't have time until after the first week in January. I will try to watch your talk page. I have finally gotten used to the Wikipedia, I write there, they answer on my talk page threading of converations when I run across whole messes of folks who do it the more sensible way. KP Botany 03:08, 27 December 2006 (UTC)
Hi there, me again. I was having a look at proteasome and thought I should ask you something since you're apparently its most eager contributor. I came across PDB: 2F16 today and wondered if you were aware of it; it's the structure of an S. cerevisiae proteasome with bortezomib bound, and I thought a close-up of an active site with bortezomib might make a nice addition to the "Proteasome inhibitors" section and/or the bortezomib article. I'm going for something like this ( Tim's work) or this (mine). I've had mixed success so far (my PC keeps crashing), but if you think it could complement the article I'll keep trying (or drop a line on Protein request?). Thanks and sorry for the rant, Fvasconcellos 23:43, 29 December 2006 (UTC)
P.S.: Feel free to move this to Talk:Proteasome if you feel it's more appropriate there.
Oh damn, I forgot to even put the boron in the legend. The
new version (slightly different crop because I moved the window by mistake :) has it yellow - odd color for boron, I suppose, but it stands out from the carbons now. It'll be on FAC soon. No, it's on FAC
now :) Thanks for pointing out this structure! Because Splette's diagrams were already there when the collaboration started, I never really went through the PDB for proteasomes.
Opabinia regalis
02:36, 3 January 2007 (UTC)
Previously I've copied stuff onto this site, is there anything that still needs dealing with? TimVickers 16:50, 31 December 2006 (UTC)
I reverted this edit of yours [1] because this image is the one that also appears on the main page, and thus should be marked with {{ mprotected}} instead of {{ mprotected2}}. Thanks. Zzyzx11 (Talk) 00:24, 1 January 2007 (UTC)
My mistake on the revert in Evolution. :: Colin Keigher ( Talk) 03:23, 4 January 2007 (UTC)
Thank you for the consideration you gave to my RfA. To be chosen as an administrator requires a high level of confidence by a broad section of the community. Although I received a great deal of support, at this time I do not hold the level of confidence required, and the RfA did not pass. Yours was one of the neutral votes, and raised concerns. I am more than willing to discuss those concerns with you if you are interested. Please let me know. Sincerely, -- BostonMA talk 13:07, 4 January 2007 (UTC)
Hi O!
Thanks so much for your excellent review of Laplace-Runge-Lenz vector! :D As always, you hit the nail on the head with the Kepler problem, which had been nagging me for some time, but which I'd been too lazy to fix. :( I'll tackle it in a few days, along with a well-intended counter-review of Proteasome — it looks great! I realized that I'd forgotten about improving the cutaway diagram; should I still try to do that? I think I can lash PyMol into behaving; being a hemi-demi-semi-Coordinatrix has its advantages! ;)
Speaking of which, if ClockworkSoul stays away for a longer time, do you want to volunteer to shoulder some of the responsibilities, along with me? Tim has a lot on his platter already, and might appreciate the help and your organizational powers. Split several ways, the work might not be too onerous? Besides, I can think of no one more clued in, competent and altogether suited to be a Coordinatrix than you. ;) ClockworkSoul seems to be recovering well, though, so maybe we don't need to worry about it.
My little niece is still very young — too young to really learn how to knit, at least from this teacher :( — but my intuition is that she won't be a biochemist, but rather an artist, judging from her furious drawing. ;) Princesses are a common theme running through her oeuvre hitherto, but perhaps I can coax her to make a ribbon diagram? ;)
I've been laid low by a ferocious and remarkably tenacious cold (I think), one of my worst ever. An unwelcome guest, it doesn't seem to want to go away, and keeps getting ruder. :( In books and opera, being consumptive is so fashionable and cool, but the reality is a lot more — phlegmatic. ;) It's ironic that I should contribute to immune system when my own is being so lame.
Trying to stay cheery and thinking of you all, Willow 13:37, 4 January 2007 (UTC)
I'm just about to crash, but I noticed your reply and couldn't leave without saying Hi in real time :)
I'll try my best scorpion on PyMol tomorrow and see what I can do. Thanks for the tutorial! :) If you have any special wishes on how it should looks, please leave instructions as detailed as possible; I'm not very intuitive about that! :(
A lot has indeed changed on immune system and, I think, for the better. Tim's really good at making a silk purse out of my sow's ear prose, and there's a wonderfully collaborative feeling there; a lot of people are contributing, mutually helping each other — Wikipedia at its best. :) I just added a skeletal draft of one section, though, that may tax even Tim's powers. ;) BTW, do you know anything about the age dependence of the immune system?
Oh, that reminds me! Check out the {{ Explain template}}; maybe it'd be an alternative way to do the glossary? I tried it out for fun at immune system for "eukaryote" but it got reverted today (not to worry, T!). It's not ideal, though, since the normal wikilink mouseover function dominates; one needs good coordination to position the mouse just so to see the Template mouseover text. Sweet dreams and get well yourself, Willow 04:02, 5 January 2007 (UTC)
Oh, had I power to execute my apprehended wishes, I would whip some programs with scorpions and lash proteins into ribbons...
Sigh. PyMol whipped me more than the reverse. So much for my dom career. ;)
I got the selections to work well, but I was stymied by the apparently simple operation of adjusting the atom sphere size independently for the alpha subunits and the active site residues. Then the program seemed to freeze up and not allow me to change any atom sizes; so I was stuck with 5 Angstroms.
FWIW (see, I'm learning!), the file is Image:Proteasome_cutaway_PyMol.png. I gave it more of a "looking from above" feel to accentuate the depth.
I'll e-mail you the PyMol session file and the cutaway PDB file, so you can play with them yourself; you'll probably have more luck. :)
Sick again, I may have overdone it today. :( Willow 01:04, 6 January 2007 (UTC)
P.S. Drat. I can't e-mail you the files since they're too big. Umm, so to make the PDB file, you'll want to delete chains H, M, N, 1 and 2 from 1G0U. Once uploaded into PyMol, you can generate selections for rings 1-4 by
select alpha_ring1, chain a+b+c+d+e+f+g
select alpha_ring2, chain o+p+q+r+s+t+u
select beta_ring1, chain i+j+k+l
select beta_ring2, chain v+w+x+y+z
The alpha subunit centroids can be selected by
select alpha_subunits1, alpha_ring1 and resi 137 and name cb
select alpha_subunits2, alpha_ring2 and resi 137 and name cb
while the active-site residue can be selected by
select active_site1, beta_ring1 and resi 1 and name ca
select active_site2, beta_ring2 and resi 1 and name ca
Then you can "show" the atoms of the latter four selections as spheres, and hide the lines of the first four selections. Color at will. Then use
set sphere_scale=3.0
to get a more decorous 3 Angstrom sphere. I'm not sure how to work it together with selections, though. :( <- Bummed Willow 01:21, 6 January 2007 (UTC)
create active_site1, beta_ring1 and resi 1 and name ca
instead of "select...". You can then change the sphere size for each object separately with set sphere_scale=3.0, active_site1
. The session file is about 19MB if you want it - is that too big?I just discovered that Sweater design is up for deletion! :( Could you help me understand what they're objecting to, and how I might fix it? I think sweater design is a valid encyclopedic topic, having been studied and described by many important fashion designers. How would it be any different from architecture or boat design? Confused and unhappy Willow 21:01, 7 January 2007 (UTC)
PS. Is there an AfD page where people are going to vote on its fate? I couldn't make that out from the template. I'd like to postpone a vote until there's a chance to salvage the article.
Please help, Sweater design is now officially Afd. Today is a bad day for me, too. :( Willow 12:39, 8 January 2007 (UTC)
PS. I added some stuff to Immune system about the computational prediction of antigenicity, but I didn't have any references. It seems right up your alley — could you help there, too? Thanks!
I am still pretty confused about this deletion business. I have had one article speedied and then userfied for me by Killerchihuahua. It is at User:Filll/Peter Cusack. I am still do not understand what was so wrong about it. Although it is a stub, This guy is a
I disagree with the statement of Wales that we have all the articles we need and all we have to do is improve what we have. Just the last couple of days:
I do not claim Peter Cusack is so important. Not like Rimmer or Bonner. At least not yet anyway. But wow the aggressive deleting. I fought like crazy to keep Hinduism and creationism the last few days and I barely managed to keep it (but had to make a lot of compromises). And I fought quite a pitched battle over Support for evolution which will probably survive with a name change. For a while it looked like that would go down in flames too. I just get tired of this. And I am still not so sure what the rules even are.-- Filll 01:53, 8 January 2007 (UTC)
DGG 04:22, 8 January 2007 (UTC)
I've been looking for prior discussions on this topic. Dragons flight thought you might have started a thread on this at one of the village pumps (policy or proposals, probably) in the last couple months. If that's so, or if you know of a discussion, could you give me a pointer/link to it? Thanks. John Broughton | Talk 13:34, 8 January 2007 (UTC)
Opabinia, where do you stand on that Object? If you need help converting them in order to address the Object, I can help. Am I missing something, or would we actually have to do every one by hand? I can't find a database that can be used to automate it - if you feel it has to be done, we can divide up the work. I still resist the idea, since it would take a lot of manual work, and the PMID should suffice, but if you need help, I'll dig in. SandyGeorgia ( Talk) 16:14, 8 January 2007 (UTC)
I have replied to this at some length just now , on User talk:Circeus. My own favorite is J electroanal chem inter electrochem, but the real gems are the changes in Crasp and JchemSoc. DGG 06:18, 9 January 2007 (UTC)
Could you please review my response to you on FAC for Folding@home. Thank You.-- Foundby 16:25, 8 January 2007 (UTC)
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The Barnstar of Good Humor | |
I Award you with this Barnstar for being a light-spirited Wikipedian whose unshakably good humor, consistently and reliably lighten the mood, defuse conflicts, and make the Wikipedia a generally better place to be. Foundby 15:18, 9 January 2007 (UTC) |
![]() |
Thank you for your support in my my RfA, which passed with a tally of 117/0/1. I hope that my conduct as an admin lives up to the somewhat flattering confidence the community has shown in me. I have no intention of letting my additional duties as a sysop detract from my article writing, and I will continue to contribute heavily to mainspace in my area of interest. Please don't hesitate to leave a message on my talk page should you need anything or want to discuss something with me.-- Nilf anion ( talk) 16:26, 9 January 2007 (UTC) |
The more the merrier, no? You deserve so much credit for
proteasome; such an important subject, so well-written and so wonderfully digestible... It's a gift to us all. Happy third helping of "you're awesome" pie :)
Willow
13:28, 10 January 2007 (UTC)
Have replied to your oppose on my rfa. I hope that is OK. → Aza Toth 03:02, 10 January 2007 (UTC)
Yeah, I thought so too as soon as I realized that Foundby started his account in less than a week after Records was blocked. User:Foundby was blocked as a result of the checkuser request. Guess we should speedy the FAC nomination for Folding@Home too. AZ t 23:33, 10 January 2007 (UTC)
Hi O,
I'm so happy that you liked the painting; it's cute, no? It made me think of us and smile; you're the one with the crown.
You're probably busy now, too, but I'm having trouble with the Encyclopædia Britannica — or rather, trouble with myself, which you might be able to help with. You'll probably laugh, but I'm having trouble controlling some seriously snarky impulses. I guess I feel a little too strongly about some things, because I can't seem to find alternate wordings for certain noteworthy facts. Usually, my brain is swimming with alternate wordings, a cage of little birds where I can reach in and grab the one I want; so it's pretty significant to me that I'm frozen. Anyway, I really want to bring this article to FA sometime, but I want it to be NPOV, broadly acceptable and, more importantly to me, a worthy article, noble in word and thought. Can you help when you have a chance? Sections that are nagging at me include the "2nd version of the 15th edition" section of the History, and perhaps the Contributors section and a few others that will likely leap out at you. There's no rush, but i would be very grateful, Willow 22:38, 11 January 2007 (UTC)
PS. I may go to bed early tonight, so that I can clear my head about it, and start afresh tomorrow.
Amazing. There actually is such a thing. Good idea to totally remove the history and create from scratch. Fan-1967 01:49, 14 January 2007 (UTC)
Peripheral membrane protein The
Molecular and Cellular Biology WikiProject's current
Collaboration of the Month article is
Peripheral membrane protein. |
– Clockwork Soul 18:54, 14 January 2007 (UTC)
I was under the impression that most of the "double redirects" were taken care of. A quick glance through the what links here at Levels of support for evolution seems to confirm this. -- ScienceApologist 18:14, 15 January 2007 (UTC)
Dear Opabinia,
I like your rework of the article Gene. Maybe we can make this article feature standard again. I realise you are not a fan of statement headings as common in some textbooks, e.g. you changed "The genome contains most genes of an organism" to "The genome". I would like to argue that the longer statement headings are more thought-stimulating than the word headings you used. But I realise that this is a matter of taste. Maybe you can explain your preference for short headings.
Also, I would like to ask why you deleted the section on the evolving concepts of the gene without integration, replacement or comment? Or did I overlook it? I think it's very interesting information and the most up-to-date part of the article. Please explain.
Best, Jasu 11:13, 18 January 2007 (UTC)
After your work on gene, will you be working on Gene Gene the Dancing Machine ?-- Filll 02:39, 19 January 2007 (UTC)
Hi there, thanks for the comments on the Trans fat FAC. I am a bit concerned with the article organization proposed, and I have a suggestion over there that I'd appreciate some feedback on. Thanks! -- cmh T C 13:52, 19 January 2007 (UTC)
Thank you for the comments on my talk page. My recent work has only cited scholarly work, and linked the ancient texts (from which Ahmes and the RMP were constructed). It may appear that my personal analysis is attached to this linking up of documents, a step that others have oddly not attempted. However, I have no idea where current and future reviews of the Middle Kingdom texts will take the discussion of ancient Eguyptian mathematics. That is, each document makes little sense - read as an independent event.
What I do know, and anyone can read, several Wikipedia posters have oddly placed their personal stamps on their writing, strongly suggesting in myopic ways, considering only one text, or one set of facts, that scribes like Ahmes did not know every much. Why are you not complaining about this Wikipedia inconsistency, and obvious scholarly error?
One day I'd like to publish additional papers on Egyptian arithmetic, one that actually redefines subtraction and division as scribes thought and wrote. Today these and other math topics have been seriously garbled, as you may have seen. For now, I'll continue to link the texts, and allow Wikipedia members determine for themselves the meaning of a particular text and its relationship to its parents, brothers, sisters and children texts. Milogardner 14:22, 20 January 2007 (UTC)
A response to your comment on my talk page has been completed. Thanks for the suggestions. Milogardner 01:46, 22 January 2007 (UTC)
Sure, no problem. A few questions though:
I'll be working on them while you decide :) so drop me a line when you get this, and I'll upload the relevant one for your appreciation. Damn, I hope I can make this accurate ;) Fvasconcellos 14:31, 20 January 2007 (UTC)
Hello. Re your vote at the article's original AFD, you might like to comment at the AFD for its recreation. Cheers. The JPS talk to me 00:54, 21 January 2007 (UTC)
I have just completed Bees and toxic chemicals and if you would cast your expert eye on it and see if I have made any gross mistakes I would be grateful. I gather it will probably get featured in "Did You Know" in the next day or two, so it is best if I do not say anything too outrageous in it.-- Filll 01:22, 21 January 2007 (UTC)
No wonder you gave Baby Gender Mentor such as detailed review. I didn't realize until just now that you are part of the Molecular Biology WikiProject. Thank you very much for your time and contributions to Wikipedia:Featured article candidates/Baby Gender Mentor. You raised many excellent points. I have made numerous changes to the article. I also made a detailed reply to you at Wikipedia:Featured article candidates/Baby Gender Mentor. If you read my reply, you will see that a couple of your questions cannot be defnitively answered at this point. For instance, I explain my understanding about Acu-Gen's relationship to BioTronics. Unfortunately, no one source comes right out and says that Wang is running Acu-Gen from inside BioTronics building, so but I am being careful to stick with the sources and not to venture into drawing my own conclusion, which would be original research. Even on this point, I think I was able to make the known connection more clear. So, with this and the other changes I made, I feel I have addressed all your points.
I would be much in your debt if you could take another look. I hope you can now support the article for FA. If not, I hope you will comment furhter so that I may continue to improve the article up to FA standard. Best regards, Johntex\ talk 10:04, 21 January 2007 (UTC)
I personally would have preferred not to define intoxication, and at some point in the future I might remove it. The reason it is there (and several other sort of silly things as well) is to try to "immunize" the article against AfD to a certain extent. For about a week I asked "bee experts" and a few "writing experts" repeatedly for their opinions, and that was one of the demands from one of the people who was pretty negative about the article. I had 3 or 4 people who gave me a list of demands, sometimes with an only semi-veiled threat of AfD. So, I tried to accommodate everyone. Even if I personally disagreed. Because you cannot really write what you think is a reasonable article here with the threat of AfD. And then of course one has editing by others. I will say that most of the edits since it was moved out of the sandbox I have agreed with, but some I do not. I think it is best to let people have their say and see how it evolves. At least now I hope it avoids AfD. I really find those AfD things tiresome. So that is why the definition is there, and a few other peculiarities as well.-- Filll 13:15, 21 January 2007 (UTC)
Maybe. But I have had enough of AfDs, so I want to do whatever I can to avoid them.-- Filll 02:36, 22 January 2007 (UTC)
This is to thank you for your early support on my RfA, which closed favorably this morning. I appreciate the confidence the community has placed in me and am looking forward to my new responsibilities. Please let me know if ever you have any comments or suggestions, especially as I am learning how to use the tools. And as for your comment that "it's about time," I guess I figured it was better to wait awhile too long than run a few weeks too early, but in any event it's done now. I look forward to working with you as a colleague. Best regards, Newyorkbrad 17:47, 21 January 2007 (UTC)
Hey, so you should check out this, which can be spruced up or paired if it would help you. Thanks for the help on Macropædia, too; I don't always see the right course sometimes. :( You also might've noticed that some cquotes escaped the recent conflagration and are beginning to proliferate again in the EB articles. ;) Hoping that you forgive my fondness for cartoons, affectionate Willow 00:34, 23 January 2007 (UTC)
Hey O!
Thanks for using the picture at alpha sheet, which I'd never heard of before but which seems really cool. Did you want a pair of them H-bonded? I also wasn't sure about the proper choice of dihedrals; the strand has a slight bend even at -45°, -45° (the smallest I tried); should it be straight? I was a little surprised that repetition of one pair of dihedral angles and then its opposite didn't give something straight (from symmetry), but maybe it's a by-product of the Cα chirality and the slight asymmetries in the Engh&Huber bond geometry? BTW, the peptide dihedral angle ω was exactly 180° (trans).
I tried out {{ bquote}} at History of the Encyclopædia Britannica; I like the attribution aspect, but I kind of miss the dramatic swashes on either side that signal the quotation. Drama queen, what can I say? ;D I'm waiting for others to say what they like there.
If you have some time, I could really use an impartial insight at Talk:Micropædia; thanks! Hoping all's well with you, Willow 02:18, 24 January 2007 (UTC)
![]() |
As you set out for
Ithaka, hope the voyage is long Don't expect Ithaka to make you rich. Ithaka gave you the
marvelous journey |
Any comments at the talk page of level of support for evolution? -- Filll 20:12, 25 January 2007 (UTC)
Sorry about the revert, I thought it was a cleverly disguised vandalism, as I didn't know the term existed. -- Wirbelwindヴィルヴェルヴィント ( talk) 05:43, 27 January 2007 (UTC)
I really think this article needs pretty much entirely rewritten to remain a FA. There is just too much wrong with it, imo, to improve it. I keep looking at it, and I just don't see it improving much in its basic form. I will be glad to review it over the days and add comments if you have time to repair it, but I don't have time until after the first week in January. I will try to watch your talk page. I have finally gotten used to the Wikipedia, I write there, they answer on my talk page threading of converations when I run across whole messes of folks who do it the more sensible way. KP Botany 03:08, 27 December 2006 (UTC)
Hi there, me again. I was having a look at proteasome and thought I should ask you something since you're apparently its most eager contributor. I came across PDB: 2F16 today and wondered if you were aware of it; it's the structure of an S. cerevisiae proteasome with bortezomib bound, and I thought a close-up of an active site with bortezomib might make a nice addition to the "Proteasome inhibitors" section and/or the bortezomib article. I'm going for something like this ( Tim's work) or this (mine). I've had mixed success so far (my PC keeps crashing), but if you think it could complement the article I'll keep trying (or drop a line on Protein request?). Thanks and sorry for the rant, Fvasconcellos 23:43, 29 December 2006 (UTC)
P.S.: Feel free to move this to Talk:Proteasome if you feel it's more appropriate there.
Oh damn, I forgot to even put the boron in the legend. The
new version (slightly different crop because I moved the window by mistake :) has it yellow - odd color for boron, I suppose, but it stands out from the carbons now. It'll be on FAC soon. No, it's on FAC
now :) Thanks for pointing out this structure! Because Splette's diagrams were already there when the collaboration started, I never really went through the PDB for proteasomes.
Opabinia regalis
02:36, 3 January 2007 (UTC)
Previously I've copied stuff onto this site, is there anything that still needs dealing with? TimVickers 16:50, 31 December 2006 (UTC)
I reverted this edit of yours [1] because this image is the one that also appears on the main page, and thus should be marked with {{ mprotected}} instead of {{ mprotected2}}. Thanks. Zzyzx11 (Talk) 00:24, 1 January 2007 (UTC)
My mistake on the revert in Evolution. :: Colin Keigher ( Talk) 03:23, 4 January 2007 (UTC)
Thank you for the consideration you gave to my RfA. To be chosen as an administrator requires a high level of confidence by a broad section of the community. Although I received a great deal of support, at this time I do not hold the level of confidence required, and the RfA did not pass. Yours was one of the neutral votes, and raised concerns. I am more than willing to discuss those concerns with you if you are interested. Please let me know. Sincerely, -- BostonMA talk 13:07, 4 January 2007 (UTC)
Hi O!
Thanks so much for your excellent review of Laplace-Runge-Lenz vector! :D As always, you hit the nail on the head with the Kepler problem, which had been nagging me for some time, but which I'd been too lazy to fix. :( I'll tackle it in a few days, along with a well-intended counter-review of Proteasome — it looks great! I realized that I'd forgotten about improving the cutaway diagram; should I still try to do that? I think I can lash PyMol into behaving; being a hemi-demi-semi-Coordinatrix has its advantages! ;)
Speaking of which, if ClockworkSoul stays away for a longer time, do you want to volunteer to shoulder some of the responsibilities, along with me? Tim has a lot on his platter already, and might appreciate the help and your organizational powers. Split several ways, the work might not be too onerous? Besides, I can think of no one more clued in, competent and altogether suited to be a Coordinatrix than you. ;) ClockworkSoul seems to be recovering well, though, so maybe we don't need to worry about it.
My little niece is still very young — too young to really learn how to knit, at least from this teacher :( — but my intuition is that she won't be a biochemist, but rather an artist, judging from her furious drawing. ;) Princesses are a common theme running through her oeuvre hitherto, but perhaps I can coax her to make a ribbon diagram? ;)
I've been laid low by a ferocious and remarkably tenacious cold (I think), one of my worst ever. An unwelcome guest, it doesn't seem to want to go away, and keeps getting ruder. :( In books and opera, being consumptive is so fashionable and cool, but the reality is a lot more — phlegmatic. ;) It's ironic that I should contribute to immune system when my own is being so lame.
Trying to stay cheery and thinking of you all, Willow 13:37, 4 January 2007 (UTC)
I'm just about to crash, but I noticed your reply and couldn't leave without saying Hi in real time :)
I'll try my best scorpion on PyMol tomorrow and see what I can do. Thanks for the tutorial! :) If you have any special wishes on how it should looks, please leave instructions as detailed as possible; I'm not very intuitive about that! :(
A lot has indeed changed on immune system and, I think, for the better. Tim's really good at making a silk purse out of my sow's ear prose, and there's a wonderfully collaborative feeling there; a lot of people are contributing, mutually helping each other — Wikipedia at its best. :) I just added a skeletal draft of one section, though, that may tax even Tim's powers. ;) BTW, do you know anything about the age dependence of the immune system?
Oh, that reminds me! Check out the {{ Explain template}}; maybe it'd be an alternative way to do the glossary? I tried it out for fun at immune system for "eukaryote" but it got reverted today (not to worry, T!). It's not ideal, though, since the normal wikilink mouseover function dominates; one needs good coordination to position the mouse just so to see the Template mouseover text. Sweet dreams and get well yourself, Willow 04:02, 5 January 2007 (UTC)
Oh, had I power to execute my apprehended wishes, I would whip some programs with scorpions and lash proteins into ribbons...
Sigh. PyMol whipped me more than the reverse. So much for my dom career. ;)
I got the selections to work well, but I was stymied by the apparently simple operation of adjusting the atom sphere size independently for the alpha subunits and the active site residues. Then the program seemed to freeze up and not allow me to change any atom sizes; so I was stuck with 5 Angstroms.
FWIW (see, I'm learning!), the file is Image:Proteasome_cutaway_PyMol.png. I gave it more of a "looking from above" feel to accentuate the depth.
I'll e-mail you the PyMol session file and the cutaway PDB file, so you can play with them yourself; you'll probably have more luck. :)
Sick again, I may have overdone it today. :( Willow 01:04, 6 January 2007 (UTC)
P.S. Drat. I can't e-mail you the files since they're too big. Umm, so to make the PDB file, you'll want to delete chains H, M, N, 1 and 2 from 1G0U. Once uploaded into PyMol, you can generate selections for rings 1-4 by
select alpha_ring1, chain a+b+c+d+e+f+g
select alpha_ring2, chain o+p+q+r+s+t+u
select beta_ring1, chain i+j+k+l
select beta_ring2, chain v+w+x+y+z
The alpha subunit centroids can be selected by
select alpha_subunits1, alpha_ring1 and resi 137 and name cb
select alpha_subunits2, alpha_ring2 and resi 137 and name cb
while the active-site residue can be selected by
select active_site1, beta_ring1 and resi 1 and name ca
select active_site2, beta_ring2 and resi 1 and name ca
Then you can "show" the atoms of the latter four selections as spheres, and hide the lines of the first four selections. Color at will. Then use
set sphere_scale=3.0
to get a more decorous 3 Angstrom sphere. I'm not sure how to work it together with selections, though. :( <- Bummed Willow 01:21, 6 January 2007 (UTC)
create active_site1, beta_ring1 and resi 1 and name ca
instead of "select...". You can then change the sphere size for each object separately with set sphere_scale=3.0, active_site1
. The session file is about 19MB if you want it - is that too big?I just discovered that Sweater design is up for deletion! :( Could you help me understand what they're objecting to, and how I might fix it? I think sweater design is a valid encyclopedic topic, having been studied and described by many important fashion designers. How would it be any different from architecture or boat design? Confused and unhappy Willow 21:01, 7 January 2007 (UTC)
PS. Is there an AfD page where people are going to vote on its fate? I couldn't make that out from the template. I'd like to postpone a vote until there's a chance to salvage the article.
Please help, Sweater design is now officially Afd. Today is a bad day for me, too. :( Willow 12:39, 8 January 2007 (UTC)
PS. I added some stuff to Immune system about the computational prediction of antigenicity, but I didn't have any references. It seems right up your alley — could you help there, too? Thanks!
I am still pretty confused about this deletion business. I have had one article speedied and then userfied for me by Killerchihuahua. It is at User:Filll/Peter Cusack. I am still do not understand what was so wrong about it. Although it is a stub, This guy is a
I disagree with the statement of Wales that we have all the articles we need and all we have to do is improve what we have. Just the last couple of days:
I do not claim Peter Cusack is so important. Not like Rimmer or Bonner. At least not yet anyway. But wow the aggressive deleting. I fought like crazy to keep Hinduism and creationism the last few days and I barely managed to keep it (but had to make a lot of compromises). And I fought quite a pitched battle over Support for evolution which will probably survive with a name change. For a while it looked like that would go down in flames too. I just get tired of this. And I am still not so sure what the rules even are.-- Filll 01:53, 8 January 2007 (UTC)
DGG 04:22, 8 January 2007 (UTC)
I've been looking for prior discussions on this topic. Dragons flight thought you might have started a thread on this at one of the village pumps (policy or proposals, probably) in the last couple months. If that's so, or if you know of a discussion, could you give me a pointer/link to it? Thanks. John Broughton | Talk 13:34, 8 January 2007 (UTC)
Opabinia, where do you stand on that Object? If you need help converting them in order to address the Object, I can help. Am I missing something, or would we actually have to do every one by hand? I can't find a database that can be used to automate it - if you feel it has to be done, we can divide up the work. I still resist the idea, since it would take a lot of manual work, and the PMID should suffice, but if you need help, I'll dig in. SandyGeorgia ( Talk) 16:14, 8 January 2007 (UTC)
I have replied to this at some length just now , on User talk:Circeus. My own favorite is J electroanal chem inter electrochem, but the real gems are the changes in Crasp and JchemSoc. DGG 06:18, 9 January 2007 (UTC)
Could you please review my response to you on FAC for Folding@home. Thank You.-- Foundby 16:25, 8 January 2007 (UTC)
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The Barnstar of Good Humor | |
I Award you with this Barnstar for being a light-spirited Wikipedian whose unshakably good humor, consistently and reliably lighten the mood, defuse conflicts, and make the Wikipedia a generally better place to be. Foundby 15:18, 9 January 2007 (UTC) |
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Thank you for your support in my my RfA, which passed with a tally of 117/0/1. I hope that my conduct as an admin lives up to the somewhat flattering confidence the community has shown in me. I have no intention of letting my additional duties as a sysop detract from my article writing, and I will continue to contribute heavily to mainspace in my area of interest. Please don't hesitate to leave a message on my talk page should you need anything or want to discuss something with me.-- Nilf anion ( talk) 16:26, 9 January 2007 (UTC) |
The more the merrier, no? You deserve so much credit for
proteasome; such an important subject, so well-written and so wonderfully digestible... It's a gift to us all. Happy third helping of "you're awesome" pie :)
Willow
13:28, 10 January 2007 (UTC)
Have replied to your oppose on my rfa. I hope that is OK. → Aza Toth 03:02, 10 January 2007 (UTC)
Yeah, I thought so too as soon as I realized that Foundby started his account in less than a week after Records was blocked. User:Foundby was blocked as a result of the checkuser request. Guess we should speedy the FAC nomination for Folding@Home too. AZ t 23:33, 10 January 2007 (UTC)
Hi O,
I'm so happy that you liked the painting; it's cute, no? It made me think of us and smile; you're the one with the crown.
You're probably busy now, too, but I'm having trouble with the Encyclopædia Britannica — or rather, trouble with myself, which you might be able to help with. You'll probably laugh, but I'm having trouble controlling some seriously snarky impulses. I guess I feel a little too strongly about some things, because I can't seem to find alternate wordings for certain noteworthy facts. Usually, my brain is swimming with alternate wordings, a cage of little birds where I can reach in and grab the one I want; so it's pretty significant to me that I'm frozen. Anyway, I really want to bring this article to FA sometime, but I want it to be NPOV, broadly acceptable and, more importantly to me, a worthy article, noble in word and thought. Can you help when you have a chance? Sections that are nagging at me include the "2nd version of the 15th edition" section of the History, and perhaps the Contributors section and a few others that will likely leap out at you. There's no rush, but i would be very grateful, Willow 22:38, 11 January 2007 (UTC)
PS. I may go to bed early tonight, so that I can clear my head about it, and start afresh tomorrow.
Amazing. There actually is such a thing. Good idea to totally remove the history and create from scratch. Fan-1967 01:49, 14 January 2007 (UTC)
Peripheral membrane protein The
Molecular and Cellular Biology WikiProject's current
Collaboration of the Month article is
Peripheral membrane protein. |
– Clockwork Soul 18:54, 14 January 2007 (UTC)
I was under the impression that most of the "double redirects" were taken care of. A quick glance through the what links here at Levels of support for evolution seems to confirm this. -- ScienceApologist 18:14, 15 January 2007 (UTC)
Dear Opabinia,
I like your rework of the article Gene. Maybe we can make this article feature standard again. I realise you are not a fan of statement headings as common in some textbooks, e.g. you changed "The genome contains most genes of an organism" to "The genome". I would like to argue that the longer statement headings are more thought-stimulating than the word headings you used. But I realise that this is a matter of taste. Maybe you can explain your preference for short headings.
Also, I would like to ask why you deleted the section on the evolving concepts of the gene without integration, replacement or comment? Or did I overlook it? I think it's very interesting information and the most up-to-date part of the article. Please explain.
Best, Jasu 11:13, 18 January 2007 (UTC)
After your work on gene, will you be working on Gene Gene the Dancing Machine ?-- Filll 02:39, 19 January 2007 (UTC)
Hi there, thanks for the comments on the Trans fat FAC. I am a bit concerned with the article organization proposed, and I have a suggestion over there that I'd appreciate some feedback on. Thanks! -- cmh T C 13:52, 19 January 2007 (UTC)
Thank you for the comments on my talk page. My recent work has only cited scholarly work, and linked the ancient texts (from which Ahmes and the RMP were constructed). It may appear that my personal analysis is attached to this linking up of documents, a step that others have oddly not attempted. However, I have no idea where current and future reviews of the Middle Kingdom texts will take the discussion of ancient Eguyptian mathematics. That is, each document makes little sense - read as an independent event.
What I do know, and anyone can read, several Wikipedia posters have oddly placed their personal stamps on their writing, strongly suggesting in myopic ways, considering only one text, or one set of facts, that scribes like Ahmes did not know every much. Why are you not complaining about this Wikipedia inconsistency, and obvious scholarly error?
One day I'd like to publish additional papers on Egyptian arithmetic, one that actually redefines subtraction and division as scribes thought and wrote. Today these and other math topics have been seriously garbled, as you may have seen. For now, I'll continue to link the texts, and allow Wikipedia members determine for themselves the meaning of a particular text and its relationship to its parents, brothers, sisters and children texts. Milogardner 14:22, 20 January 2007 (UTC)
A response to your comment on my talk page has been completed. Thanks for the suggestions. Milogardner 01:46, 22 January 2007 (UTC)
Sure, no problem. A few questions though:
I'll be working on them while you decide :) so drop me a line when you get this, and I'll upload the relevant one for your appreciation. Damn, I hope I can make this accurate ;) Fvasconcellos 14:31, 20 January 2007 (UTC)
Hello. Re your vote at the article's original AFD, you might like to comment at the AFD for its recreation. Cheers. The JPS talk to me 00:54, 21 January 2007 (UTC)
I have just completed Bees and toxic chemicals and if you would cast your expert eye on it and see if I have made any gross mistakes I would be grateful. I gather it will probably get featured in "Did You Know" in the next day or two, so it is best if I do not say anything too outrageous in it.-- Filll 01:22, 21 January 2007 (UTC)
No wonder you gave Baby Gender Mentor such as detailed review. I didn't realize until just now that you are part of the Molecular Biology WikiProject. Thank you very much for your time and contributions to Wikipedia:Featured article candidates/Baby Gender Mentor. You raised many excellent points. I have made numerous changes to the article. I also made a detailed reply to you at Wikipedia:Featured article candidates/Baby Gender Mentor. If you read my reply, you will see that a couple of your questions cannot be defnitively answered at this point. For instance, I explain my understanding about Acu-Gen's relationship to BioTronics. Unfortunately, no one source comes right out and says that Wang is running Acu-Gen from inside BioTronics building, so but I am being careful to stick with the sources and not to venture into drawing my own conclusion, which would be original research. Even on this point, I think I was able to make the known connection more clear. So, with this and the other changes I made, I feel I have addressed all your points.
I would be much in your debt if you could take another look. I hope you can now support the article for FA. If not, I hope you will comment furhter so that I may continue to improve the article up to FA standard. Best regards, Johntex\ talk 10:04, 21 January 2007 (UTC)
I personally would have preferred not to define intoxication, and at some point in the future I might remove it. The reason it is there (and several other sort of silly things as well) is to try to "immunize" the article against AfD to a certain extent. For about a week I asked "bee experts" and a few "writing experts" repeatedly for their opinions, and that was one of the demands from one of the people who was pretty negative about the article. I had 3 or 4 people who gave me a list of demands, sometimes with an only semi-veiled threat of AfD. So, I tried to accommodate everyone. Even if I personally disagreed. Because you cannot really write what you think is a reasonable article here with the threat of AfD. And then of course one has editing by others. I will say that most of the edits since it was moved out of the sandbox I have agreed with, but some I do not. I think it is best to let people have their say and see how it evolves. At least now I hope it avoids AfD. I really find those AfD things tiresome. So that is why the definition is there, and a few other peculiarities as well.-- Filll 13:15, 21 January 2007 (UTC)
Maybe. But I have had enough of AfDs, so I want to do whatever I can to avoid them.-- Filll 02:36, 22 January 2007 (UTC)
This is to thank you for your early support on my RfA, which closed favorably this morning. I appreciate the confidence the community has placed in me and am looking forward to my new responsibilities. Please let me know if ever you have any comments or suggestions, especially as I am learning how to use the tools. And as for your comment that "it's about time," I guess I figured it was better to wait awhile too long than run a few weeks too early, but in any event it's done now. I look forward to working with you as a colleague. Best regards, Newyorkbrad 17:47, 21 January 2007 (UTC)
Hey, so you should check out this, which can be spruced up or paired if it would help you. Thanks for the help on Macropædia, too; I don't always see the right course sometimes. :( You also might've noticed that some cquotes escaped the recent conflagration and are beginning to proliferate again in the EB articles. ;) Hoping that you forgive my fondness for cartoons, affectionate Willow 00:34, 23 January 2007 (UTC)
Hey O!
Thanks for using the picture at alpha sheet, which I'd never heard of before but which seems really cool. Did you want a pair of them H-bonded? I also wasn't sure about the proper choice of dihedrals; the strand has a slight bend even at -45°, -45° (the smallest I tried); should it be straight? I was a little surprised that repetition of one pair of dihedral angles and then its opposite didn't give something straight (from symmetry), but maybe it's a by-product of the Cα chirality and the slight asymmetries in the Engh&Huber bond geometry? BTW, the peptide dihedral angle ω was exactly 180° (trans).
I tried out {{ bquote}} at History of the Encyclopædia Britannica; I like the attribution aspect, but I kind of miss the dramatic swashes on either side that signal the quotation. Drama queen, what can I say? ;D I'm waiting for others to say what they like there.
If you have some time, I could really use an impartial insight at Talk:Micropædia; thanks! Hoping all's well with you, Willow 02:18, 24 January 2007 (UTC)
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As you set out for
Ithaka, hope the voyage is long Don't expect Ithaka to make you rich. Ithaka gave you the
marvelous journey |
Any comments at the talk page of level of support for evolution? -- Filll 20:12, 25 January 2007 (UTC)
Sorry about the revert, I thought it was a cleverly disguised vandalism, as I didn't know the term existed. -- Wirbelwindヴィルヴェルヴィント ( talk) 05:43, 27 January 2007 (UTC)