For my research, to create neat images of the molecules I study, I use
Pymol. It's free, part of
Debian, command-driven, very powerful and it produces really good-looking pictures. Although, admittedly, if you don't buy a subscription, the documentation is rather sparse. I'm using scripts to generate ray-traced pictures, but I can't include the
ray command directly in the scripts, as
Pymol would not give me the opportunity to change anything before tracing (and things I trace take loads of time...). So I write a
ray command, but I comment it out, such as in the following example,
cytochrome.pml:
load http://www.rcsb.org/pdb/files/1c6s.pdb
hide everything
show sticks, (resname HEC)
color orange, (resname HEC)
show cartoon
bg_color white
set_view (\
0.939850032, 0.167392358, 0.297758341,\
0.336208642, -0.299271941, -0.892972171,\
-0.060366094, 0.939367712, -0.337551534,\
0.000000000, 0.000000000, -106.161231995,\
33.668910980, -4.749122620, -24.822664261,\
-9.742469788, 222.064941406, 0.000000000 )
# ray 800,800
So, to easily generate PNG images from such a file, I wrote the following
makefile snippet, that does the job (as demonstrated by the figure on the right, produced by this very snippet ran on the
cytochrome.pml file above):
%.png: %.pml
cd $(dir $<); \
ray_trace_args= grep -o 'ray.*' $(notdir $<) tail -n1 egrep -o '([0-9, ]+)' sed 's/ //g' ; \
pymol -c -d "@$(notdir $<)" -d "cmd.ray($$ray_trace_args)" -g $@
I hope this snippet will prove useful for others. At any rate, it will prove useful for me ! Just for the record, this protein, represented in
cartoon
view, is called cytochrome c
6 and is one of the proteins implied in the photosynthesis of some organisms.
I first played World of Goo on the Wii. I loved it. Great stuff, reminded me a little of Lemmings, but way way better. Today I found out it s also available for Linux, and I immediately downloaded it. I was pleased to see a 
From tomorrow, if you start seeing bugs or getting email about your packages where the version string ends in em[0-9], or where dependencies mentioned by reportbug include such a version suffix, the user is running one of the two Emdebian distributions to be released alongside lenny (and based on lenny packages). You might also see Emdebian in the output of 'apt-cache policy' if your bug reports request or supply such data.
I was at this event back in November and they ve just emailed me this week to point out 
So, 
Since several month, 
From the local paper, yesterday, in a larger article about the bushfires
roaming hither and yon:
It is funny the way things work out when you're looking for help.
Recently I was working on a Ruby + FUSE based filesystem and as part of the development I added simple diagnostic output via trivial code such as this:
Of course, I was in Brussels this week-end, for FOSDEM. I gave a talk about 
This year I managed to go to fosdem every day, even at the beer event. Not that I attended many talks: I was quite busy getting the network to work. We got wireless in almost all locations in the end. Setting up and fixing the problems took most of Saturday. On Sunday we added the final 'experimental' room via a wireless bridge link across the square, with the beam over the heads of the people in the queue for Belgian fries.
I'm supporting a class of high school students who are new to programming, and will be learning some python. Most of these students are comfortable with computers, but not hacker types, and few if any of them have written code before. I'm looking for an editor or an Integrated Development Environment (IDE) that won't be too scary for them, and will help them get used to the novel idea of writing code without simultaneously having to get used to the novel idea of an unfamiliar user interface. So i can't expect them to pick up my beloved emacs, for example. But on the other end of the spectrum, i'd hate for them to try to write python in an word processor (i've seen people do it!). Here's what i think i'm looking for: