I just added app-shells/fish to the tree. It’s a shell with syntax highlighting, awesome tab completion, and more. The tab completion for man pages, for example, actually includes the description of the command from whatis.

Look at the screenshots.

Update: More cool stuff about fish: It has really good error reporting, so it’s easy to find problems. If you type ‘help’ in the shell, it opens a browser (an X-based browser if DISPLAY is set, otherwise something like links/lynx) — This is cool because you get hyperlinks. Reworked syntax for much of the shell scripting features is self-consistent and easy to understand.

Yesterday I added WebMO to the tree. Here’s a few screenshots so you can see how it looks (Click for a bigger version.).

I don’t think the webapp-config hook script works properly, so you may need to fix all the paths in globals.int that point to /usr/share. globals.int is at /var/www/localhost/cgi-bin/webmo/interfaces/globals.int on a standard installation. The correct paths:

cgiBase="/var/www/localhost/cgi-bin/webmo"
htmlBase="/var/www/localhost/htdocs/webmo"
userBase="/var/www/localhost/webmo"

Also, I don’t think reinstallations work properly yet. They may overwrite your configuration from old installations. That’s why it’s in package.mask.

To log in for the first time, visit ${HOST}/cgi-bin/webmo/login.cgi. Username admin, blank password.

Here’s the “home screen.” It shows info on all the jobs you’ve run, and you can selectively view certain jobs.

You can actually rotate the molecule, see vibrational modes, and so forth in the viewer. Also if you’ve calculated a spectrum, you can pop up a picture of it.

This is where you select the type of job you want to run. Some of the programs have much more complex sets of options than Tinker.

Today I added two new molecular graphics packages — viewmol and gOpenMol. I’m working on tinker, a molecular mechanics package. So far, it installs everything to locations that make sense — and you’d be amazed how much work that was. But I haven’t tested how it runs yet, and that will surely require more fixes. I’m probably going to install WebMO tomorrow, so I have a consistent way to test tinker that doesn’t involve the CLI. That also raises the question of getting a WebMO ebuild together, which I’ll also work on.

In case you haven’t guessed, finals are next week so my procrastination kicked into high gear in the past day or two.

Update (12/3): Tinker’s now added and works great, except for FFE, the X-java front-end. This gives Gentoo a strong, free platform for computational chemistry from molecular mechanics (tinker) through semi-empirical calculations (mopac7) to quantum mechanics (gamess). Soon, I hope to add WebMO, the user-friendly front-end to all three in addition to some proprietary programs such as Gaussian.

First, there was that broken file in the digest, because I had downloaded an older version but it got updated on the mirrors.

Next, my middle clicks to open URLs don’t work. That in itself is enough to convince me to downgrade, because it’s critical to not wasting tons of time erasing and re-pasting URLs in the address bar. I’ll try looking for answers this weekend, but if I don’t find any, back to 1.0 I go.

That sucks. They’re only keeping Linux in a special “hacker’s model”, the WRT54GL. So starting with series 5, don’t buy the WRT54G if you expect to get Linux on it.

I had some Costco gift cards to use, and my digital camera’s been slowly dying for a year (even faster since getting soaked by the ocean in Hawaii). So I bought a new Canon SD500, a nice 7MP camera. I found a couple of docs saying it works in Linux. Problem is, I just can’t get it working.

First, it wasn’t even recognized as the user but was as root (found using `lsusb`), so I figured it was some sort of permissions problem. I came across a post from some guy named Steve suggesting that hotplug was the problem. After looking into it further, I found a file ‘/etc/hotplug/usb/usbcam’ that defines a group required to access hotplugged USB things. In Gentoo, this group is called “plugdev” — never heard of it in my life, never seen it in any documentation, nothing. You’d expect that it might be the “usb” group, but no, it’s something with a weird name nobody’s ever heard of.

Next, the camera was found in f-spot (added to portage today) and gthumb, but I still can’t get photos to import because other errors are coming up. The camera won’t respond to repeated identifier sequences, or it isn’t recognized, or something else.

If someone else has a Canon SD500 working properly in Linux, particularly Gentoo, please let me know.

Highly recommended reading: federico’s post on his experiment with firefox, X and compressed images.

I’ve been subscribed to the RSS feed for O’Reilly Radar for a while, but this is by far the most interesting thing I’ve seen on it. It’s a series of 15 or so testimonials (so far) from “alpha geeks” on how they got into computers in the first place.

I just finished “Memories of Ice,” book three of Steven Erikson’s Malazan Book of the Fallen series. Whenever I get the chance, I’m a voracious fantasy/sci-fi reader, so I have a tough time finding new, good books that I haven’t read yet.

Erikson’s series really highlights the kind of thing I love to find. On Saturday, I was up in Portland and stopped by Barnes & Noble while we were at the mall. I spotted the latest book in the series and snatched it up. Most of Sunday, I was reading and got through around 600 pages. (For those of you who don’t know me, I generally read about 100 pages an hour.) I finished up the last 200 pages or so yesterday.

I went to sleep around 11 last night. When I woke up, I had 512 spam in my inbox.

That’s gone beyond acceptable, even considering that my local spam filter caught all but 9. Five more showed up while I was writing this.