Talk:Transcription preinitiation complex

message: there should also be a diagramatic representation of these factors.
I would name it Transcription preinitiation complex, because for e.g. translation PIC exists too!  —Preceding unsigned comment added by 130.79.76.47 (talk) 08:47, 17 June 2009 (UTC)
thread_title: Untitled

message: Hi again folks. I have become mired in another real-life game. In my sandbox, the last sentence I added linked to Pioneer factor. So, I spent considerable time learning about pioneer factors, then looked at the wp page and gasped. I understand that I've composed some stinkers, but the images are terrible - the condensed chromatin depiction made me lol! The textual content needs correcting and updating and lots of it. I'm very reluctant to even link to the page from my PIC sandbox page. I'd like to ask for advice. Do you folks think I should make a fairly detailed description of pioneer factors and their function in the PIC article and not link to the pioneer factor page, or should I update the pioneer factor page first? My inclination, based on masochism and the desire to have more reason to eat peanuts, is to update pioneer factor page first so as to avoid duplications later on between PIC and PF articles, but I am open to being talked out of it. Also, one of the major authors in the pioneer factor research arena is a guy name Ken Zaret, and he and I were both in Fred Sherman's lab together. We weren't close friends, I haven't seen or talked to him in over 30 years, and I don't think that me mentioning his work is a COI, but I want to make sure that nobody would object. Thanks for any comments. DennisPietras (talk) 02:53, 4 March 2017 (UTC)
replies: text: I actually rather like the clarity of those images. They're completely unrealistic, but they show the parts neatly and cleanly. I also like peanuts, though, so what do you think of a nicer version of those pictures done in Blender 3D, with DNA shown as a double helix, some slightly more realistic-looking histones, but still not too complex in shape, and some semi-convincing transcription factors? I could even do an animation with dramatic lighting. It'll be great, the audience will love it. --Slashme (talk) 15:29, 4 March 2017 (UTC)

text: Whoops, forgot to answer the other questions. What you don't want is to be accused of doing a WP:CFORK, so if you publish this page and it overlaps massively with the Pioneer Factor page, and contradicts it, that could be a Bad Thing™. Knowing someone who was a major researcher in an area isn't a CoI, as long as you're not egregiously promoting his work. The main test is "can you write neutrally about the topic", and in this case, I'm sure the answer is yes. --Slashme (talk) 15:37, 4 March 2017 (UTC)
replies: text:  Please take a moment to look at the graphical abstract at http://www.cell.com/abstract/S0092-8674(12)01298-6 What I had my heart set on (and notice how "rough" they drew the tf's!!! I could have done that!) was to use the condensed chromatin part of your white image and have an image of a sock (boghog would have loved it!) representing a Sox protein pushing its toe into the chromatin and distorting it a bit. Then have an image of a microphone (indicating cMyc protein) coming in next to the sock and knocking a nucleosome off completely to generate the nucleosome free region. I'm guessintg that it isn't your style but if you want to do an animation, that would obviously be fantastic! Re: CFORK. Thanks! More reason to tackle pioneer factor and more peanuts first! DennisPietras (talk) 21:12, 4 March 2017 (UTC)

text: Sock and microphone, eh? Nice mental image, but as you guessed, not quite my style ;-] I've been working in Blender a bit, and I already have a nice cartoony DNA strand unwrapping from a histone complex that I based on a PDB structure, with the histone morphing from its normal shape with spikes holding onto the DNA to something a bit smoother, so that the DNA can slip off. I'm quite happy to add Sox and cMyc into the mix, and ideally, I'd like to grab some structures off PDB, so that they will be realistic. As I see from the Sox article, it binds to the minor groove of DNA, which is apparently how it disloges the DNA from the histone? I'm not very clear about where I should bring it into the animation, though. cMyc is basically discussed as a gene promotor: they don't mention what it does to push away the nucleosome. Based on the short video clip that I've included, you might have some more detailed suggestions on how to script it. --Slashme (talk) 19:29, 5 March 2017 (UTC)
replies: text:  AMAZING VIDEO! 2 general "problems" quickly before supper. 1) You mistakenly think that wp articles are up-to-date  and, 2) can you slow down the video? I'll write more after dinner. Thanks, DennisPietras (talk) 21:46, 5 March 2017 (UTC)
replies: text: Sure, no problem. I'd made it quick because less frames mean less render time, but I'll leave it running when I go to bed now, and you'll have a video with twice the resolution and twice as slow tomorrow. --Slashme (talk) 23:12, 5 March 2017 (UTC)
replies: text:  Well, I'm glad that you get to sleep with all you have going on! Since you are determined to make this more realisitic, I'm going to copy some images from your video and find better example proteins since the sock and microphone are out. I'll e-mail jpg's to you. I feel a little bad about encouraging you to spend so much time on this, since you have a job to do, but since you're an experienced wikipedian, I'm sure you know about the risk of WikiHomelessness, which was explained to me early on by TimothyJosephWood at the teahouose! DennisPietras (talk) 01:58, 6 March 2017 (UTC)

text:  That sounds great! I see you essentially sent me a storyboard by email, so I will do the animation this week. --Slashme (talk) 08:48, 6 March 2017 (UTC)
replies: text:  Hmm...I just learned another term - storyboard. Remember, no rush! Thanks again!DennisPietras (talk) 03:12, 7 March 2017 (UTC)
thread_title:  Whac-A-Mole or rather Whac a [[Pioneer factor]] 

message: Hi slashme et al. Stimulated by slashme's work on the images, I'd like to make the orange, green and grey blobs of the transcription factors look more 3Dish, like the histones. I've got both GIMP and ImageJ on my computer, and I've tried screwing around with them, but am making no progess. Can anybody please give me some hints before I exhaust all my peanut supply? Thanks, DennisPietras (talk) 03:33, 15 March 2017 (UTC)
thread_title:  "3Dish" images