In the continuing saga of making Gentoo a great distribution for chemistry and structural biology, I’ve been packaging computational and molecular graphics applications. The latest addition to the tree is molscript, a popular program for preparing publication-quality graphics.

Other recent additions by myself and others include GAMESS, NAMD, MOLMOL, NMRPipe and MOPAC7.

With some luck and some time, we should see VMD and CCP4 in the relatively near future, among others.

I got an iPod nano for my birthday. It’s amazingly small — probably about 1/4″ thick, and 1.5″x3.5″ or so (2.54cm/inch, for those of you in the rest of the world). Now I’m trying to figure out how to get everything working nicely with Linux. Note that I don’t actually want to put Linux on the iPod, I just want to get things syncing properly.

I found a Linux Journal article from a few months back about using gtkpod as an iTunes act-alike. Also, it took a little searching, but gtkpod also provides scripts to sync the Calendar and Contacts with a number of Linux “groupware” apps. Looks like everything will work great!

Update: Brandon pointed me at a couple of other iPod apps: banshee and dopi. Banshee looks almost exactly like iTunes, and dopi is meant to be used in combination with nautilus for drag-n-drop.

So, I decided I’d like to make Gentoo a solid distro for X-ray crystallography, my specialization in biochemistry/biophysics. Unfortunately all the apps I’ve started packaging so far have build systems clearly designed and constructed by scientists.

These are the types of apps where you’re expected to source some shell script before the build starts to set up random environment variables, then compile the whole thing in-place and leave it there, source and all. It’s actually incredibly difficult to get it independent of the source, as things have cross-directory dependencies on locations of other things.

This time, it’s CCP4. Why can’t they just use autotools??

Today’s my birthday. If you appreciate what I’ve done for Gentoo, or you have a generous spirit, feel free to express that via Paypal or my Amazon wishlist. =)

My wishlist contains a number of books ranging from less than $10 to more than $100, many of which would help in Linux work, others with grad school, and a few for (gasp!) entertainment.

It was good to read in Rich Burridge’s blog that the Sun Studio compilers are now free, but then I got stopped by the roadblock of mandatory registration when I went to their page.

My definition of “free” isn’t just cost, but lack of hassle when trying to download something. Filling out a long registration form doesn’t qualify.

I couldn’t write a better headline to describe it.

“This is a sad day. We’re becoming a laughingstock of not only the nation, but of the world, and I hate that.”

Recently, anholt got the tinderbox working for modular X.

As the Pegasos that Genesi gave me holds the only place on the build page now, I encourage a few more people (especially those with interesting architectures) to jump on there. Just read the tinderbox page to get started. I recently ran a couple of days with a 2.4 kernel sparc, so that’s sort of covered. And daniels had an x86 and amd64 on there till recently, but they disappeared.

Ever want to see what I look like when I’m at a hacking session? Polvi posted a pic of our last one.

You’ll have to guess which one I am, from the labels.

So I drove up to Salem last night to try and get a deck together, because there was a tournament with a $500 prize today. Spent about $100-$150 to get the deck finished, and had high hopes of winning. But then I got taken down by this really weird POS that I don’t think could really beat anything else, but crushed my deck. And then I ran into it again 2 rounds later and lost again. Oh well.

Haven’t decided whether to tweak this deck or start something new and put this one away for a while. I ended up 2-2-1, so I’m batting .500. Too bad this isn’t baseball. But that’s an improvement from last tournament, so I’m working my way back into practice after five years off.

I highly recommend picking up Magic to anyone interested in increasing your creativity and mental agility (or for that matter, anyone interested in winning poker or blackjack). It’s like a combination of chess and art. You can even play it for free online at somewhere like magic-league.com and the #magic-league IRC channel on solidirc, using the Apprentice program. In the past few years, Magic players have stormed online poker and won millions, as well as taking away more millions at the World Series of Poker.

In other news, X.Org RC2 is all the way in portage, and seems to generally be working quite well. I’m still having issues with XKB and VT switching both being broken (perhaps related? who knows.), but nobody else filed bugs about it so maybe I’m the only one.

Haven’t done a whole lot of Gentoo work lately besides the RC2 bumps on Friday. Trying to focus on classes and research for a while, in hopes of getting decent grades this quarter and not getting kicked out of grad school. Would be a bit annoying to have to job search, despite the many options I have with my multi-tined background, since we’re mostly living paycheck to paycheck.

The second release candidate for modular X began hitting the tree about 15 minutes ago. It should be complete later today.

For future reference, here’s the code I use to copy and commit all the ebuilds from my overlay. Run it from the category level.

cvs="/usr/local/share/gentoo-x86/"
cat="x11-libs/"
msg="Bump for 7.0RC2."
for i in */*.ebuild; do ip=${i%/*}; iv=${i#*/}; iv=${iv%.ebuild}; cp ${i} ${cvs}${cat}${ip}/; cp ${ip}/files/digest-${iv} ${cvs}${cat}${ip}/files/; pushd ${cvs}${cat}${ip}/; cvs add ${iv}.ebuild files/digest-${iv}; echangelog "${msg}"; repoman ci -m "${msg}"; popd; done