Evolutionary pathways

A bit of grass applied to a megaprim, some commercial pathway textures, a few labels and "Hey Presto!": the evolution of mycobacteria based on the presence or absence of so-called regions of difference. Less is more.

Protein meshes in five easy pieces

Caveat: I know nothing about meshes except, (big) perhaps, how to make them for molecules...

We all have to start somewhere and in my case the first faltering steps were at least straightforward:

1. Install the molecule viewer UCSF Chimera. File|Fetch by ID a structure, e.g. 1rex, from the PDB.
   
2. Change the Presets to ribbons and File|Export Scene in .x3d format (.wrl works too).
3. Install meshlab (pictured above), File|Open the .x3d file and, if required, colour and simplify it (there's a lot to play with on the Filters menu that will only make sense after more detailed investigation; for example, Clustering decimation under Remeshing has a fairly radical effect in terms of reducing vertex count/file size while maintaining overall shape).
4. Save in .dae format (aka COLLADA)
5. Import into Second Life and rez or, in my case, wait patiently for full SL implementation.

Not being in the beta programme, I know nothing about SL (or any other kind of) meshes apart from what was pre-released during the temporary lifting of the NDA so the above may or may not be of any use at all. In particular, I don't know how the final file plays with the multiple levels of detail supported by SL and, of course, the prim-equivalent limitation likely to be imposed. Creating appropriate UV map textures is also going to be a headache for anything complex unless it can be automated, as per Hiro Sheridan's sculpted protein service. I'm also clueless as to whether Viewer 1.23 support is being retrofitted. Making the meshes interactive or animated is also going to be interesting, as per the multi-sculpted proteins.

Only time (or someone on the beta programme) will tell if the above is feasible. Quality-wise, there is doubtless much to assimilate. However, if the method does work, it is well within the compass of students.

SL Shared media presentation

Bit of a tired ramble -- I'd anticipated originally that I would do a more engaging version live in Second Life but it would have overrun even more than it does now. No script so there are bound to be some errors and omissions, not to mention errs and umms (or are they the same things?). I'll do some screencasts in due course to show how the apps work (or would work if they were finished!). This is also my first use of authorStream for this kind of thing.

There are acknowledgements for the media on the last slide. Open Access is wonderful.