Molecules in motion...

...across grids, that is.

To celebrate publication of the paper by Andy Lang and Jean-Claude Bradley on Chemistry in Second Life, I thought I'd use Meerkat to take one of the molecules generated by Andy's older molecule rezzer into an OpenSim grid. This is Intel's ScienceSim (the Galileo sim, to be precise) and, as you can see, Meerkat ported and linked the 145 prim molecule (basically a peptidoglycan monomer) without problems. I'm not entirely sure how the molecule was positioned (possibly in the same position it was originally archived) but it was easy enough to track down using the mini-map. Bear in mind that Meerkat at least does not port scripts and other inventory contents, though a separate trial showed that it could archive and import one of Andy's protein sculpted prims inside SL.

Interesting times.

Here's a protein I made earlier...

One of the things I've wanted to do this year is make it easier for the students to generate something tangible within a 50 min session. This means taking the "Blue Peter" approach of explaining the preliminary steps ("Here's one I made earlier"), giving them the resources derived from them (textures, scripts) and asking them to assemble the final version, in this case a sculpted protein with a touch script.

The script in this case displays a dialog allowing you to swap between the three surface textures derived from Hiro Sheridan's web application plus another image, in this case derived from UCSF Chimera (by the way, setting a transparent background in Chimera involves using the Tools|Viewing Controls|Effects dialog). Inspired by Simone Gateaux's blog, this image (the upper one in the accomanying figure) is actually a particle and automatically orients towards the avatar camera (though, alas, the image represents just one static view at present). Although this means no additional prims were involved, even temporarily, it can be a little confusing that this second image does not respond to touch so it times out.

Other options include delivering a notecard (named About; the students write this, of course), displaying hovertext (entered via the Description field; ditto), rotating (times out automatically), offering a map teleport, and linking to a web page (in this case determined by appending the object name, i.e. the gene id, to the appropriate path on the KEGG database DBGET utility). The dialog is not very tolerant of mistakes: it depends very much on students sticking to a naming regime for the different resources, e.g. the particle image in this case was the rather unmemorable MT0067_5. The map teleport involves the students locating the gene on the giant M. tuberculosis genome, setting a landmark there and copying the latter into the contents of the sculpted protein.

Hopefully the students still get some sense of achievement (quite a few got to a finished version). Seeing students on the giant genome at last was certainly great for me. Even if it is still somewhat incomplete, it has a sense of presence all of its own (OK, I may be a little biased!).