## Tuesday, February 10, 2009

### A makefile snippet for generaring ray-traced images from pymol

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 c6 and is one of the proteins implied in the photosynthesis of some organisms.

## Sunday, February 8, 2009

Quite a fair amount of time has flown since my decision to implement an emacs mode for the proposed machine-readable format for debian/copyright files. A have to admit that I had left that sleeping for quite a long while. But I took my courage, and rewrote nearly everything I had done so far. I'm quite happy with the results, to be truthful. The debian-mr-copyright-mode features:
• syntax highlighting
• a coverage mode show all files in the package, including the ones not covered by the copyright file
• the coverage mode shows which glob matches a given file
• it provides links to visit files and go to the declaration leading to a given label
The aim of this mode is to provide a quick check for uncovered files in a package, and also means to verify if the license of a file is not misrepresented.

git clone git://git.debian.org/git/users/fourmond/debian-mr-copyright-mode.git