You = Graham Mills

[15:05] You: The Forensic Science group sounds interesting, Kem. What do you do?
[15:06] Kem Writer: Forensic science students observe/participate in the roleplaying of crimes and their investigatioin....
[15:06] Asorel Todriya: CSI for SL?
[15:06] You: Real crimes or fictional
[15:07] You: Hi Pathfinder!
[15:07] Kem Writer: We are devising tools to record trace evidence transfer.....
[15:07] Hiro Sheridan: Hi Pathfinder
[15:07] You: Welcome!
[15:07] Pathfinder Linden: greetings folks :)
[15:07] Kem Writer: At the moment simple crime scenarios....
[15:07] Asorel Todriya: Hi Pathfinder. Pleasure to have a Linden with us :)
[15:08] You: Grab a seat -- don't mind me -- I'm a bit laggy
[15:08] Pathfinder Linden: pleasure is all mine.
[15:08] Kem Writer: (Hello Pathfinder) In the future possibly re-enactments of unsolved crimes, cold cases
[15:09] Pathfinder Linden: that's fascinating, Kem. so as you said, reconstructing scenes of unsolved crimes in SL is something you're looking to do?
[15:09] Asorel Todriya: so more like Crimewatch then? very cool
[15:10] Kem Writer: Yes, Pathfinder, but the main thrust at the moment is teaching crimescene forensics
[15:10] Pathfinder Linden: so like CSI, but with real education behind it. ;)
[15:10] You: The kind of thing Stan was talking about on the SLED list (but more advanced)?
[15:10] Kem Writer is taking advantage of the strong roleplaying culture in SL
[15:11] You: We should all do that
[15:11] Kem Writer: TY Hiro - an excellent idea
[15:11] Pathfinder Linden knows folks in healthcare who are interested in leveraging the role playing culture here for creating interactive cases for med students to work through
[15:12] Hiro Sheridan: Graham, is Horace or Xanthe coming?
[15:12] You: I thought Horace was coming -- Eloise said she might come too
[15:12] You: Max Chatnoir was here earlier
[15:12] Asorel Todriya: As we're 10 minutes in, I'll just say now that we don't have a specific agenda or time cut-off for this meeting, so if anyone needs to go early and wants to see or cover a particular topic, then do go ahead and let us know.
[15:12] Asorel Todriya: Thanks for coming!
[15:12] Hiro Sheridan: glad to be here :)
[15:13] Kem Writer would like a contact name from Pathfinder
[15:13] Pathfinder Linden: Kem, it's a group at Harvard Medical School. I can't recall the contact right now, but I've made a note and will give you the contact info later
[15:14] You: I'm pretty sure the people from Imperial in Scilands are doing something similar
[15:14] Kem Writer: TY Pathfinder
[15:14] Asorel Todriya: Also the Ann Myers medical center in SL are already doing that. They're creating interactive medical equipment.
[15:14] Pathfinder Linden: my pleasure, Kem
[15:14] You: Hey, we're a mine of information :)
[15:15] Pathfinder Linden: Asorel, oh excellent. I didn't know that. thanks
[15:15] Asorel Todriya: Oh yeah we're a networking success already :)
[15:15] You: lol
[15:15] Asorel Todriya: Thanks. I had a tour of the Ann Myers center a couple of months ago in conjunction with my real-life biotech networking group in NYC
[15:15] Pathfinder Linden: that's how all the amazing stuff happens in here, in my experience. getting connected to the right folks as collaborators and colleagues.
[15:16] Hiro Sheridan: yes
[15:16] Asorel Todriya: the NYC group has fairly regular meetings in SL (one last night on autism and SL)
[15:16] Kem Writer: Pathfinder you might be able to do something about this: my networking is limited by the 25 Groups
[15:16] Asorel Todriya: snap
[15:16] Hiro Sheridan: lol
[15:16] Pathfinder Linden grinds his teeth
[15:16] Pathfinder Linden: yeah, the 25 group limit sucks.
[15:17] Pathfinder Linden: unfortunately, it's a seriously non-trivial thing to increase it. but it's on our plate.
[15:17] Asorel Todriya: This group might have been folded into Dataviz a while back if I hadn't screwed up sending out the poll (thought I had but later realised that one needs to click an extra button)
[15:17] Hiro Sheridan: You can be two people in Sl and then then limit is 50 groups :)
[15:17] Pathfinder Linden: Hiro, yes, we know that lots of folks do that as a workaround
[15:17] Pathfinder Linden: but it's not an optimal solution :P
[15:17] You: I think getting ACS inworld has been a big plus too
[15:17] Hiro Sheridan: yes
[15:17] Asorel Todriya: yes, they're a good nexus
[15:18] You: We should hold our next meet there
[15:18] Hiro Sheridan: good idea
[15:18] Pathfinder Linden was very excited when he learned of their presence here
[15:18] Asorel Todriya was surprised to find himself projected onto the big screen at their annual conference IRL
[15:18] Hiro Sheridan: he he
[15:18] Pathfinder Linden: ha! congrats, Asorel :)
[15:18] Pathfinder Linden: RL organizations like that coming into SL, they bring a lot of legitimacy and networking opportunities into the space. very cool.
[15:19] You: lol -- funny when hta happens
[15:19] Asorel Todriya: I guess I'm just a poster child for Science 2.0 ;)
[15:19] You: Hiro has been pivotal in getting them setup
[15:19] Pathfinder Linden: Hiro, really? that's outstanding
[15:19] Hiro Sheridan: :) So, how about I demonstrate my rezzer - Orac?
[15:19] Asorel Todriya: that would be great
[15:19] You: Go for it -- and then explain how it differs from the others
[15:19] Hiro Sheridan: yes, I am continuing to help ACS too - red tide build next
[15:20] Hiro Sheridan: ok we're is space Graham?
[15:20] You: That's interestng -- with Andra?
[15:20] Hiro Sheridan: where
[15:20] You: Anywhere
[15:20] Hiro Sheridan: no, with one of my biology honors students
[15:20] You: How big ?
[15:20] Hiro Sheridan: not too big
[15:20] Asorel Todriya: probably best to stay near the incoming teleport point for a while in case moer people come
[15:20] Hiro Sheridan: corn field leading to a river to the ocean with a dead zone and a red tide
[15:20] Hiro Sheridan: ok
[15:20] Hiro Sheridan: i'll follow you
[15:21] You: Sounds good
[15:21] Hiro Sheridan: ok here's Orac
[15:21] You: Hiy Orac
[15:21] You: Blake 7 influence?
[15:22] Hiro Sheridan: absolutely
[15:22] You: :)
[15:22] Asorel Todriya: superb
[15:22] Hiro Sheridan: if you have ever seen Blakes' 7 then you know why he has that name
[15:22] Hiro Sheridan: just like the real orac he goes out and searches the internet for info
[15:22] Pathfinder Linden: :)
[15:22] Hiro Sheridan: and brings it back here to SL
[15:22] Orac 3.2: Please input your InChI, inchikey, or smi String
[15:22] Hiro Sheridan: smi=O=C(NCc1cc(OC)c(O)cc1)CCCC/C=C/C(C)C
[15:22] Orac 3.2: Please wait - calculating atom positions.
[15:23] Orac 3.2: number of atoms: 49
[15:23] Orac 3.2: number of bonds: 49
[15:23] Pathfinder Linden: sound effects too :) i love it
[15:23] Hiro Sheridan: ys, he talks to you
[15:23] Hiro Sheridan: same voice as the TV character :)
[15:23] Orac 3.2: Please wait - getting more data
[15:23] Orac 3.2: number of atoms: 3
[15:23] Orac 3.2: number of bonds: 1
[15:23] Pathfinder Linden: nice touch :)
[15:24] You: Good work, Orac
[15:24] Hiro Sheridan: That's capsaicin
[15:24] Asorel Todriya: which database holds the 3d coordinates?
[15:24] Asorel Todriya: that's hot :)
[15:24] Hiro Sheridan: i got the SMILES here" http://www.chemspider.com/Search.aspx
[15:24] Hiro Sheridan: no database
[15:24] Hiro Sheridan: can input any SMILES
[15:24] Asorel Todriya: ok
[15:24] Hiro Sheridan: Orac then queries 3 web services which take the SMILES and do a 3d minimization
[15:25] Asorel Todriya: that's what i meant - it's minimized
[15:25] Hiro Sheridan: I then parse the response from the web services
[15:25] Hiro Sheridan: into a form that I then send back to SL
[15:25] Asorel Todriya: seems to work very smoothly
[15:25] Hiro Sheridan: yes
[15:25] Hiro Sheridan: still Beta
[15:25] Pathfinder Linden: nice
[15:25] Hiro Sheridan: but he's not too bad
[15:25] You: Perpetual beta?
[15:25] You: V Web 2.0
[15:25] Asorel Todriya: does he link it together autmatically?
[15:25] Hiro Sheridan: he may be, because he relies on web services that I can't control :)
[15:26] You: :)
[15:26] Hiro Sheridan: I do have a version that links automatically
[15:26] Hiro Sheridan: but it takes time to link everything
[15:26] Hiro Sheridan: actually quicker to do it manually
[15:26] Asorel Todriya: ok
[15:26] Hiro Sheridan: ok name you favourite organic compund
[15:26] You: Are you still using the earlier molecule rezzer?
[15:26] Hiro Sheridan: and we'll get orac to rez it :)
[15:26] Kem Writer: 1,8-cineole
[15:27] You: How big is that?
[15:27] Hiro Sheridan: yes, I use my earlier rezzer to rez unusual thing that have elements not recognized but the web services
[15:27] Kem Writer: C10
[15:27] Graham Mills looks for hard hat
[15:27] You: I find it useful and would miss it
[15:27] Hiro Sheridan: found it on chemspider O2C1(CCC(CC1)C2(C)C)C
[15:27] Orac 3.2: Please input your InChI, inchikey, or smi String
[15:28] Hiro Sheridan: smi=O2C1(CCC(CC1)C2(C)C)C
[15:28] Orac 3.2: number of atoms: 29
[15:28] Orac 3.2: number of bonds: 30
[15:28] Orac 3.2: Please wait - calculating atom positions.
[15:28] Asorel Todriya: O=S(=O)(O)c1ccc([Hg]Cl)cc1 (pCMBS)
[15:28] Hiro Sheridan: want to try that one? has Hg in it might not work :)
[15:29] Asorel Todriya: ah ok.
[15:29] Hiro Sheridan: don't know if the web services I use know Hg but I can try
[15:29] You: N-acetyl muramic acid?
[15:29] Hiro Sheridan: let's see
[15:29] Asorel Todriya: I'm not intentionally trying to break him :)
[15:29] Hiro Sheridan: lol
[15:29] Orac 3.2: Please input your InChI, inchikey, or smi String
[15:29] Hiro Sheridan: smi=O=S(=O)(O)c1ccc([Hg]Cl)cc1
[15:29] Asorel Todriya: look what happened with HAL, and that was accidental...
[15:29] Orac 3.2: Please wait - calculating atom positions.
[15:29] Orac 3.2: number of atoms: 0
[15:29] Orac 3.2: number of bonds: 0
[15:29] Orac 3.2: Please wait - getting more data
[15:29] You: lol
[15:29] Hiro Sheridan: no he didn;t like that one
[15:30] Pathfinder Linden: lol
[15:30] Hiro Sheridan: sorry no Hg
[15:30] Asorel Todriya: ok, good to know. Sulfur is ok?
[15:30] Hiro Sheridan: should be
[15:30] Hiro Sheridan: what are you thinking?
[15:30] Hiro Sheridan: N-acetyl muramic acid?
[15:30] Asorel Todriya: O=S(=O)(SCC[N+](C)(C)C)C
[15:30] Asorel Todriya: MTSET
[15:31] Asorel Todriya: thiol-modifier
[15:31] You: Important component of bacterial cell wall
[15:31] Hiro Sheridan: ok
[15:31] Asorel Todriya: (these are compounds we use in lab)
[15:31] Hiro Sheridan: smi=O=S(=O)(SCC[N+](C)(C)C)C
[15:31] Orac 3.2: Please input your InChI, inchikey, or smi String
[15:31] Hiro Sheridan: smi=O=S(=O)(SCC[N+](C)(C)C)C
[15:31] Orac 3.2: Please wait - calculating atom positions.
[15:31] Orac 3.2: number of atoms: 27
[15:31] Orac 3.2: number of bonds: 26
[15:31] Hiro Sheridan: notice that the nuclei have the correct relative sizes too
[15:31] Hiro Sheridan: and colurs
[15:32] Asorel Todriya: that's a nice touch
[15:32] Graham Mills claps
[15:32] Pathfinder Linden: that's brilliant. and the voice feedback is simply perfect.
[15:32] Pathfinder Linden: lol
[15:32] Hiro Sheridan: lol
[15:32] You: Have you had students use it, Hiro?
[15:32] Asorel Todriya: something fun for students
[15:32] Hiro Sheridan: yes, wouldn't be as much fun to use without him talking back to you
[15:32] Hiro Sheridan: Jean-Claude uses it all the time for his organic chemistry students
[15:33] Hiro Sheridan: I am a mathematic physicist in RL
[15:33] Hiro Sheridan: mathematical*
[15:33] You: How do they find it comapred to 2.5D software?
[15:33] Hiro Sheridan: it is much better because the can then take the molecule and do things with it
[15:34] You: Yeah, I think the little bit more effort required is no bad thing -- slow learning
[15:34] You: is good
[15:34] Pathfinder Linden: plus they can interact with the molecule with other people at the same time.
[15:34] Pathfinder Linden: group learning
[15:34] Hiro Sheridan: yes Pathfinder
[15:34] You: Absolutely -- shared presence and mutual support
[15:35] Hiro Sheridan: I have linked the molecule so you can take it (I think) if you want one
[15:35] Pathfinder Linden: i always stress that fact about SL when talking to academics about the learning potential in SL around complex models like this
[15:35] Asorel Todriya: well thanks :)
[15:35] Hiro Sheridan: :)
[15:35] Pathfinder Linden: ty Hiro
[15:35] Hiro Sheridan: yw
[15:35] Asorel Todriya: actually I'm going to use that for my real research, because I'm trying to see how it fits inside one of the proteins I've rezzed in SL :)
[15:36] You: Yeah -- that's of interest to me too
[15:36] Hiro Sheridan: he he
[15:36] Pathfinder Linden: i like sitting on molecules
[15:36] Asorel Todriya: lol everyone wants to sit on them.
[15:36] Asorel Todriya: I have no idea why
[15:36] Pathfinder Linden: sulfur is nice and cushy
[15:36] Asorel Todriya: hehe
[15:37] Asorel Todriya: Mercury was apparently too slippery...
[15:37] Pathfinder Linden: lol
[15:37] Hiro Sheridan: he he
[15:37] Hiro Sheridan: yes
[15:37] Hiro Sheridan: I contacted the owner of the web service and he says it doesn;t work all the time with inorganic-type elements
[15:37] Hiro Sheridan: Rajarshi Guhu at Indiana
[15:37] Hiro Sheridan: by the way
[15:38] Asorel Todriya: it's still light-years ahead of what I had in college
[15:38] Hiro Sheridan: yes, I have been having organic chemistry nightmares
[15:38] Kem Writer: Hiro, I am interested to know if any progress has been made in representing Xray structure maps in SL - with electron densities?
[15:38] Pathfinder Linden thinks everyone has organic chemistry nightmare flashbacks
[15:38] You: :)
[15:39] Hiro Sheridan: Kem I am currently working with one of my honors students
[15:39] Hiro Sheridan: to create electron orbital exhibits
[15:39] Hiro Sheridan: sculpty ones
[15:39] Hiro Sheridan: let me see
[15:39] Kem Writer wishes his students did have organic chemistry flashbacks
[15:39] You: lol
[15:39] Pathfinder Linden: ha!
[15:40] Hiro Sheridan: That's 4fz(x^2-y^2)
[15:40] Hiro Sheridan: sculpted hydrogenic atomic orbital
[15:40] Hiro Sheridan: We're working on an exhibit
[15:40] Asorel Todriya: great idea
[15:41] Hiro Sheridan: could do the same thing with electron density maps
[15:41] You: V nice, Hiro
[15:41] You: Are the maps generated programmatically?
[15:41] Hiro Sheridan: yes, I wrote a php script to generate the sculpty maps
[15:41] Kem Writer: Any chance of being able to walk around inside a molecule - like the biological cell I've seen here somewhere?
[15:41] You: lol, I'm glad you're my friend
[15:42] Hiro Sheridan: :)
[15:42] Pathfinder Linden: when interacting with and viewing complex 3d models of things like molecules, i worry often that the built-in camera controls are too clunky for new folks in SL to really feel comfortable moving their view around. have any of you had that feedback from students in here?
[15:42] Hiro Sheridan: Yes Max's molecule is cool
[15:42] Asorel Todriya: is that the same thing that produced the sculpty of protein surfaces on the blog?
[15:42] Hiro Sheridan: Paul Burke actually next door to you at University of Western Australia
[15:42] Hiro Sheridan: has a visualization project
[15:42] Hiro Sheridan: where you can go inside molecules and crystals
[15:42] Asorel Todriya: I've rezzed some proteins on the other side of this island that you can walk around and fly in
[15:43] Hiro Sheridan: ok let's go look at Asorel's proteins
[15:43] Asorel Todriya: ok, follow me then
[15:43] Pathfinder Linden needs to explore more around here, definitely
[15:43] You: ok Kem?
[15:44] Asorel Todriya: I'm a structural biologist IRL, so my approach is somewhat different
[15:44] Pathfinder Linden: wow
[15:44] You: Scuse me, guys
[15:44] Hiro Sheridan: k Graham
[15:44] Asorel Todriya: I'm going for a slower type of build, but with aesthetics and ease of understanding as goals along with low prim count
[15:45] Hiro Sheridan: yes, my rezzer is very prim intensive :)
[15:45] You: Yeah, Asorel beats me hollow there
[15:45] Asorel Todriya: These are amino acid backbone cartoons only
[15:45] Asorel Todriya: Graham's structures have a cool interactivity that these don't
[15:46] You: So long as you have your own island and don't want more than 2
[15:46] You: :)
[15:46] Pathfinder Linden: lol
[15:46] Asorel Todriya: so I'm aiming less at teaching and more at inspiring the layperson that science is pretty
[15:46] You: They pay your salary
[15:46] Pathfinder Linden: sounds like complementary goals overall
[15:47] Asorel Todriya: yep, that's the idea.
[15:47] Pathfinder Linden: different levels of visualization and interactivity to teach different concepts and different types of learners
[15:47] Hiro Sheridan: I love the Helicase
[15:47] You: Exactly
[15:47] Asorel Todriya: thanks, that one's beautiful IMHO
[15:47] Asorel Todriya: I'm trying to do the pretty ones first.
[15:47] Hiro Sheridan: what do the varyations in color represent?
[15:47] Asorel Todriya: They of course tend to be the symmetrical ones
[15:48] Asorel Todriya: I'm experimenting with color. So far I'm hand coloring everything
[15:48] Hiro Sheridan: wow
[15:48] You: Craftsmanship
[15:48] Asorel Todriya: In the GFP, the beta barrel is yellow and the chromophore is green
[15:48] Asorel Todriya: In the MDR, I've highlighted a single subunit
[15:49] Asorel Todriya: In the adrenergic receptor, each of the classical 7 transmembrane segments is a different color
[15:49] Asorel Todriya: if there are enough prims, I'll temporarily rez the acetylcholine receptor, where I've used color to delineate functional domains
[15:49] Asorel Todriya: 1 sec
[15:50] You: Still 5K left, go for it
[15:50] Asorel Todriya: you can fly inside this one ;)
[15:50] You: That's th balloon-shaped one -- love it
[15:50] Hiro Sheridan: nice, this is the brain one right?
[15:51] Asorel Todriya: purple is the ligand binding domain, green and red in the membrane domain and yellow is cytoplasmic
[15:51] Asorel Todriya: looks good from above too
[15:51] Asorel Todriya: if you want to pretend to be an ion
[15:51] Pathfinder Linden: BE the ion!
[15:51] Asorel Todriya: yes, this is from brain and also found at the neuromuscular junction
[15:51] Pathfinder Linden: that's a beautiful model to experience from the inside
[15:51] Hiro Sheridan: I'm stuck lol
[15:51] Asorel Todriya: many of these structures have only been discovered in the last 3 years or so
[15:51] Hiro Sheridan: I got docked
[15:51] You: lol
[15:52] Hiro Sheridan: he he
[15:52] Pathfinder Linden: nice!
[15:52] Asorel Todriya: that;s about where nicotine would bind, for the smokers
[15:52] You: You can get intimate with molecules in a way not possible in 2.5D
[15:52] Asorel Todriya: absolutely
[15:52] Hiro Sheridan: cool stuff Asorel
[15:52] Pathfinder Linden: yes, fantastic Asorel
[15:52] Pathfinder Linden: it crosses the border into art
[15:53] You: That's a good thing
[15:53] Asorel Todriya: in our lab we do a lot of sequence and structure gazing, and I'm using these models to actually come up with experiments. Flying around it is inspiring in a way that even the regular modelling software doesn't provide
[15:53] Asorel Todriya: and in terms of controls, Pathfinder, more intuitive than those packages
[15:53] Pathfinder Linden: very interesting
[15:54] Asorel Todriya: yeah, thanks for SL :)
[15:54] Hiro Sheridan: lol
[15:54] You shout: Hey Eleanor, over here
[15:54] Asorel Todriya: Hi Eleanor
[15:55] Pathfinder Linden: greetings Eleanor
[15:55] Kem Writer: Hi, Eleanor
[15:55] Eleanor Fanwood: Well, greetings! The hour almost got away from me!
[15:55] You: Greetings
[15:55] Hiro Sheridan: Hi Eleanor
[15:55] Eleanor Fanwood: I looked up and suddenly.... almost over! So, my apologies for missing most of the gathering.
[15:55] Hiro Sheridan: np
[15:55] You: np -- small but very select
[15:55] Asorel Todriya: No problem, I don't think the time limit is particularly binding anyway as long as we're having fun
[15:56] Pathfinder Linden agrees
[15:56] You: I'm hoping the pix I take will be OK
[15:56] You: As a record
[15:56] Eleanor Fanwood: Without dragging the conversation aside, would someone care to IM me a short recap of what I missed? 25 words or less. LOL
[15:56] You: I'll do that
[15:56] Asorel Todriya: thanks Graham
[15:56] Eleanor Fanwood: Thanks Graham.
[15:56] You: But I have the chat transcript too
[15:56] Pathfinder Linden: whatever happened to that bubblegum device that folks at Nature give away. i liked it for its simplicity for laypeople. you could just say the name of common molecules and see them rezzed.
[15:57] Pathfinder Linden: I have one, but it stopped working a while ago.
[15:57] Hiro Sheridan: it is still on nature
[15:57] Hiro Sheridan: Second Nature is the sim
[15:57] M4 BubbleGum (Internet Enabled): Please state the name or structure id of the molecule you wish to create in chat.
[15:57] M4 BubbleGum (Internet Enabled): Searching for "glucose"...
[15:57] M4 BubbleGum (Internet Enabled): No such substance found.
[15:57] Pathfinder Linden: :P
[15:57] Asorel Todriya: it's diabetic
[15:58] Pathfinder Linden: it always does that. damnit
[15:58] Pathfinder Linden: glucose
[15:58] Pathfinder Linden: Asorel, LOL
[15:58] Hiro Sheridan: h ehe
[15:58] Pathfinder Linden: i think it is internet-disabled now
[15:58] Pathfinder Linden: ah well
[15:59] Pathfinder Linden: oh cool. ty Orac
[15:59] Pathfinder Linden: i mean ty Hiro :P
[15:59] Hiro Sheridan: yw anyone else want the latest Orac version?
[15:59] Asorel Todriya: Would love one, thanks!
[15:59] Kem Writer: Very much, Hiro
[15:59] Asorel Todriya: super
[15:59] Hiro Sheridan: should be full perms so feel free to mess with him and distribute to friends
[16:00] Eleanor Fanwood: Surely
[16:00] Pathfinder Linden: very cool.
[16:00] You: Me too pls Hiro
[16:00] Kem Writer: Thank you, Hiro
[16:00] You: Hiro can you do a quick demo for Eleanor?
[16:00] Hiro Sheridan: yw
[16:00] Hiro Sheridan: sure
[16:00] Pathfinder Linden: one thing I've wondered about...is anyone creating avatars that are of different molecular structures?
[16:00] Hiro Sheridan gave you Orac 3.2.
[16:00] Eleanor Fanwood: that would be welcome
[16:00] Pathfinder Linden: i always thought it would be fun to be a dopamine molecule floating around a synapse
[16:00] Asorel Todriya: interesting idea, Pathfinder
[16:00] Hiro Sheridan: Orac acceops SMILES Inchi and inchikey
[16:00] Orac 3.2: Please input your InChI, inchikey, or smi String
[16:01] Hiro Sheridan: so something simple
[16:01] Hiro Sheridan: smi=CC
[16:01] Orac 3.2: Please wait - calculating atom positions.
[16:01] Orac 3.2: number of atoms: 8
[16:01] Hiro Sheridan: :)
[16:01] Pathfinder Linden: could tell students "today we learn about synapses...please put on your dopamine avatars and we'll explore vesicles" and so on
[16:01] Orac 3.2: number of bonds: 7
[16:01] Kem Writer: There is every possible fetish in SL, Pathfinder!
[16:01] Asorel Todriya: I think I can imagine some kind of brownian motion demonstration :)
[16:01] Pathfinder Linden: lol
[16:01] Hiro Sheridan: he can rez ~95% of molecules on chemspider
[16:01] You: Yes Pathfinder -- they would think you were mad but I agree it's a good concept
[16:02] Hiro Sheridan: just look up the SMILES and get Orac to dynamically minimize the structure and rez it
[16:02] Pathfinder Linden: Graham, wouldn't be the first time i was thought of as mad... :P
[16:02] You: lol
[16:02] Pathfinder Linden: i think that's dopamine.
[16:02] Hiro Sheridan: he he
[16:02] Asorel Todriya: Radiolab on NPR actually did a show called "Your Brain on Love" a while back where they got audience members to 'be' different neurotransmitters, including dopamine
[16:03] Hiro Sheridan: Yes, I have a benzene halo somewhere too
[16:03] Pathfinder Linden: Asorel, really? that's interesting.
[16:03] Asorel Todriya: the whole thing devolved into a singles event, apparently
[16:03] Eleanor Fanwood: I'm feeling just slightly threatened over here by that appendage.... :)
[16:03] Pathfinder Linden: LOL
[16:03] Asorel Todriya: hehe
[16:03] You: You'll have trouble getting it off him
[16:03] You: Ah, no
[16:03] Pathfinder Linden: heh
[16:04] Asorel Todriya: I suppose you could animate that Felicene molecule, Hiro, and make it a pet that follows you around
[16:04] Asorel Todriya: I love that one
[16:04] Hiro Sheridan: yes and make it purr
[16:04] You: I was playing around trying to turn a molecule into a boat earlier
[16:04] Pathfinder Linden: molecular pet. that's a fascinating idea.
[16:04] Pathfinder Linden: Graham, nice!
[16:04] Hiro Sheridan: yes I played about using boat and chair for ACS island
[16:04] Hiro Sheridan: but wasn;t willing to compromise the correct angles
[16:04] You: lol, Hiro -- you always get there first :)
[16:05] Asorel Todriya: poly-lysine snake that hisses, etc
[16:05] Pathfinder Linden: there's something about when a learning experience has a playful and slightly surreal component to it. i've seen that happen in SL. it can really engage students, as long as focus is kept on learning goals.
[16:05] You: lol, quite happy to compromise as not a structural biologist
[16:05] Hiro Sheridan: :)
[16:05] Hiro Sheridan: yes Pathfinder, there's no rule that says students hsouldn't have fun while learning
[16:06] Asorel Todriya: lol I guess bond angles and ergonomics are doomed to be seperate fields
[16:06] Pathfinder Linden: precisely
[16:06] Eleanor Fanwood: So I am surely more of a novice here than any of you, and I am in fact not a chemist, but my chemists here have been asking if someone has built a demo in SL that will allow a molecule to change in time
[16:06] Hiro Sheridan: yes Asorel
[16:06] Hiro Sheridan: yes Eleanor
[16:06] Hiro Sheridan: Jean-Claude Bradley and I have a reaction mechanism
[16:06] Asorel Todriya: what I've seen of that it's really cool
[16:06] Hiro Sheridan: where you can step through all the intermediaries
[16:06] Eleanor Fanwood: Very nice, I'd like to see it in action sometime
[16:06] Pathfinder Linden: also, i was recently in strategy meetings about long term things we should be doing in SL to help educators specifically. one thing i made a point to mention was simply "more prims". even mentioned the work of folks like you all in molecular modeling. ;)
[16:06] Hiro Sheridan: through chat
[16:07] You: ty Pathfinder -- that would help a lot
[16:07] Asorel Todriya: seconded
[16:07] Hiro Sheridan: actually the prim limit has made us do some of the coolest stuff, like Asorel
[16:07] Asorel Todriya blushes
[16:07] Hiro Sheridan: otherwise you'd end up with huge stick and ball models :)
[16:07] Pathfinder Linden: Hiro, that's true. often hard limits force very creative solutions
[16:07] Kem Writer: Surprisingly, I have found that our Forensic Science students are not very interested in 'not-for-credit' SL activities
[16:07] You: OK, I admit to being a fake among you lot
[16:08] You: Kem, it's sad but that's how it is. Finding ways to assess what we do here will be important
[16:08] Hiro Sheridan: for example
[16:08] Asorel Todriya: I think you may be able to cancel out 'SL' from your sentence Kem, and retain the meaning. But I'm a bit of a cynic...
[16:08] Hiro Sheridan: here's a single prim protein
[16:08] Hiro Sheridan: falcipan-2
[16:09] Asorel Todriya: oh yeah that's the ticket
[16:09] Eleanor Fanwood: my goodness!
[16:09] You: Nice
[16:09] Pathfinder Linden: Hiro, very cool. yeah, that's a good example of a use for sculpties we never even thought of.
[16:09] You: Can you texture it at all?
[16:09] Asorel Todriya: I've played around with using sculpties too
[16:09] You: lol, me too with zero success
[16:09] Hiro Sheridan: yes, I have written a php script that converts a pdb file into a sculpty map
[16:10] Asorel Todriya: That's a hand-built alpha helix cartoon, lol
[16:10] Asorel Todriya: but it's one prim
[16:10] Hiro Sheridan: http://slusage.com/sculpties/
[16:10] Pathfinder Linden: Asorel, very cool
[16:11] Pathfinder Linden: Asorel, gotcha
[16:11] Hiro Sheridan: So Eleanor, I can show you the reaction mechanism another day if you like
[16:11] You: We can sav it for the next meet on ACS?
[16:11] Hiro Sheridan: good idea Graham
[16:12] Hiro Sheridan: excellent idea in fact
[16:12] You: Maybe see Andra's stuff too?
[16:12] Eleanor Fanwood: Yes, let's do that, Hiro, and thanks.
[16:12] Asorel Todriya: yep, it seems we have plenty to talk about and do
[16:12] Asorel Todriya: I want to see those pets, Hiro :)
[16:12] Pathfinder Linden seconds that request
[16:12] Eleanor Fanwood: I'm going to point several of the folks here at that website, Hiro, thanks
[16:12] Hiro Sheridan: yes, I'd like to see Horace, and Xanthe and Eloise there too :)
[16:12] Hiro Sheridan: yw
[16:12] Asorel Todriya: Do we know anyone from the NIH who is in SL?
[16:13] Asorel Todriya: They have all the money...
[16:13] Hiro Sheridan: lol
[16:13] Pathfinder Linden: i've got to head out. thanks so much for inviting me to this meeting. please let me know about the next one. you're giving me a lot of food for thought.
[16:13] You: Shall we take a quick peak at my stuff?
[16:13] Asorel Todriya: Thanks Pathfinder, so good to see LL interested
[16:13] Hiro Sheridan: bye Pathfinder, good to see you
[16:14] You: Another time, Pathfinder -- tahnks for coming
[16:14] Asorel Todriya: yep, bring it on Graham
[16:14] Hiro Sheridan: sure Graham
[16:14] Pathfinder Linden: my pleasure. have a great weekend everyone. see you again soon!
[16:15] You: lol, I seem to be sinking into the megaprim
[16:15] Asorel Todriya: must be the Lindens bending Second-spacetime
[16:15] You: If you want the background, take the notecard from the purple prim next to me
[16:15] MystiTool HUD 1.0.23: Entering chat range: Kem Writer (18m)
[16:16] You: This isn't molecular but maybe worth showing -- it's called StoryMachine
[16:16] Hiro Sheridan: cool Graham, you should put a landmark in the notecard
[16:16] Controller whispers: Graham Mills chose 'Bloom+>'.
[16:16] Controller whispers: WELCOME TO BLOOM 0.1 [1]
[16:16] You: It rezzese nodes dynamically from a script in a notecard
[16:16] You: It's intended for novice avatars
[16:16] Hiro Sheridan: cool
[16:16] You: No prim-handling required
[16:17] You: The nodes are interactive
[16:17] Recognizing whispers: Please touch again (known bug)
[16:17] Hiro Sheridan: he he
[16:17] Recognizing: Changing level Up
[16:17] Recognizing: Changing level Down
[16:17] Asorel Todriya: it's gonna blow!
[16:17] Explaining whispers: Please touch again (known bug)
[16:17] You: Anyways, onwards
[16:17] Hiro Sheridan: cool Graham
[16:17] Disk: Listening...
[16:18] You: This is part of a class on bacterial pathogenicity
[16:18] You: Demonstrates how bacteria and host proteins fight it out
[16:19] You: But also says something strangely about the scientific method
[16:19] You: Anyway, one of the enzymes is the classic lysozyme found in tears
[16:19] You: So the structure next to the eye is its substrate -- part of the glycan chain that holds bacteria together
[16:20] Asorel Todriya: i like the translucent blocks marking the functional domains. Clever.
[16:20] You: While we've know for a long time the chemical composition of peptidoglycan, the arrangement of th strands is still in doubt
[16:20] You: The basic unit is a dimer of two sugars caleld Nam and Nag
[16:21] You: We have three sugars here, another NAM and you cans ee there's a slight twist
[16:21] You: At the top
[16:21] You: Made this using Hiro's molecule rezzzer
[16:21] Hiro Sheridan: see the double bonds give it away :)
[16:21] You: Anyway, turns out that the twist is actually 120 degrees
[16:22] You: When you add on the peptides that crosslink the strands
[16:22] You: And that suggestss a very different model to the conventional idea that the strands wrap round the cell
[16:22] You: viz that they are perpendicular to the cell and form a mesh
[16:22] You: Which is what we see here
[16:23] Asorel Todriya: this is so cool to see as a progression
[16:23] Hiro Sheridan: yes, very cool stuff
[16:23] You: k -- I said I was interested in lysozyme -- this is it in full prim, but no side chain, mode
[16:23] You: As Asorel said, it's a tad interactive
[16:23] Atom: :60:N:ASN
[16:23] Asorel Todriya: I think the 2d cartoon on the right is an extremely useful reference to compare with the 3d model
[16:24] You: Yep -- did that in UCSF Chimera
[16:24] You: You can also use the console
[16:24] Hiro Sheridan: two-sided
[16:24] Hiro Sheridan: see that?
[16:24] You: Pretty, lol
[16:25] Asorel Todriya: it's feeling very Christmassy in here all of a sudden
[16:25] Hiro Sheridan: lol
[16:25] You: The amino acids are color-coded
[16:25] Eleanor Fanwood: lol
[16:25] You: This is a failed attempt at a walk-thru version
[16:25] You: 5 slices done using chimera again
[16:26] Hiro Sheridan: clever
[16:26] You: But still fun and something I want to play with a bit more
[16:26] Asorel Todriya: it's almost there I think
[16:26] Asorel Todriya: neat idea
[16:26] You: You can go all the way through
[16:26] You: Might be better with environment set to midnight
[16:27] Eleanor Fanwood: spacey
[16:27] You: I think I also want to play around with followcams
[16:27] You: And this is a larger protein that bacteria have nabbed from multicellular oragnisms such as ourselves
[16:28] Hiro Sheridan: what do you mean nabbed?
[16:28] Asorel Todriya: you could get Orac to make some vancomycin to inhibit all this :)
[16:28] You: We use proteases to attack bacteria and they've grabbed one of our protease inhibitors
[16:28] You: I mean lateral gene transfer at some stage
[16:28] Asorel Todriya: they're sneaky little
[16:28] You: This is one I'd like to animate
[16:28] Hiro Sheridan: we caused the gene transfer?
[16:29] You: Basically it's a protease trap
[16:29] You: Um, no -- probably ages ago, lol
[16:29] Hiro Sheridan: he he
[16:29] Hiro Sheridan: phew
[16:29] You: Anyway, that's almost it
[16:29] Eleanor Fanwood: nice work!
[16:30] You: Just to say, as some of you know, that there's a protein rezzing toolkit and a website as per the notecard
[16:30] Asorel Todriya: very immersive
[16:30] You: I hope so :)
[16:30] You: ty
[16:30] Hiro Sheridan: great Graham
[16:30] Kem Writer: Thank you very much, Graham - I am afraid I have to leave right away!
[16:30] Asorel Todriya: bye, Kem, thanks for coming!
[16:30] You: np -- nice to see you Kem
[16:30] Hiro Sheridan: I actually should go too
[16:30] Hiro Sheridan: bye Kem
[16:30] Kem Writer: Goodbye all - I look forward to next time!
[16:30] You: Sorry to have kept you all, we did over-run a tad
[16:31] You: Next time = ACS
[16:31] Hiro Sheridan: np, wanted to see it
[16:31] Hiro Sheridan: bye for now
[16:31] You: Bye Hiro
[16:31] Asorel Todriya: fantastic stuff, folks
[16:31] Asorel Todriya: see you around soon I'm sure
[16:31] Hiro Sheridan: yes ACS next time, I nominate Asorel as chair :)
[16:31] Eleanor Fanwood: I'm needing to leave also, but I'm very glad I stopped in!
[16:31] You: Bye Eleanor
[16:31] Eleanor Fanwood: I'll be watching for the next meeting and will try to arrive on time instead. :-) Be well, all!
[16:31] You: lol, bfn