Random Encounters

88724 scary phone message
2010-08-18

Just now, my (not very fancy) phone showed the following corrupted message to me:

I'm a bit at a loss about what is going on? If you have any idea, I would be happy to receive hints via email. Do I need to worry?

52851 using DSSP in the "bio3d" R package
2010-08-04

The program DSSP is used to determine the secondary structure of a protein, taking the three dimensional coordinates of its atoms as the input. Bio3d is a library for the statistical software package R which makes it easier to analyse protein structure; as part of this, bio3d contains an interface to DSSP (in the function dssp). Since I had a bit of trouble using this interface, here are some hints.

1. Get the DSSP program from the DSSP webpage. For academic use, the program is free of charge, but you need to fill in a license agreement.
2. Rename the executable to dssp (mine was called DSSP_MAC.EXE after I had downloaded it).
3. Move the file to the directory where it will live. For my system (and for the examples below) I chose /usr/local/bin/. The name of this directory is not allowed to contain white space.
4. Call the dssp function with this directory as the exepath argument. The value of the exepath argument must end in / (on Linux/Unix/MacOS) or \ (on Microsoft Windows). Also note that every \ in an R string constant needs to be doubled, e.g. on Microsoft Windows you will probably need to write something like exepath="C:\\path\\to\\file\\".

Example. In R one can now use the following commands.

library("bio3d")
pdb <- read.pdb("12as")
x <- dssp(pdb, exepath="/usr/local/bin/")

Then the secondary structure information of the protein 12AS can be accessed as follows:

> x$helix
$start
  1   2   3   4   5   6   7   8   9   1   2 
  5  76 130 170 182 258 277 297 320 271 310 

$end
  1   2   3   4   5   6   7   8   9   1   2 
 27  83 155 176 193 268 283 305 325 275 312 

$length
 1  2  3  4  5  6  7  8  9  1  2 
23  8 26  7 12 11  7  9  6  5  3 

$chain
 [1] "A" "A" "A" "A" "A" "A" "A" "A" "A" "A" "A"

This tells us that the first helix reaches from residue 5 to residue 27 (both inclusive).

73630 cereal grains
2010-08-03

I learned about the different kinds of grains long ago, when I was in primary school. Since then I have somehow managed to confuse myself about which grain is which. Here's to unconfusion! (All information and pictures are from Wikipedia; follow the links for details.)

name	picture	comments
wheat / Weizen (Triticum aestivum, Triticum durum, etc.)		Used for bread, flour, couscous, beer, biofuel, … Needs good soil and climate, several species of wheat are used, main source of vegetable protein in human food.
barley / Gerste (Hordeum vulgare)		Used for beer, whisky, animal feeding, … One of the first cultivated crops (together with einkorn and emmer).
oat / Hafer (Avena sativa)		Used for animal feeding (e.g. horses), oat flakes, porridge, … Can be grown in regions with relatively cold, wet summers.
rye / Roggen (Secale cereale)		Used for bread, animal feeding, … Can grow on relatively poor soil and in colder climates.

33420 new puzzle game
2010-06-27

In the last days I have finished my first ever browser-based game: a puzzle, based on the classical fifteen puzzle. Cou can play the game here and download the source code from the program's homepage.

73972 punting
2010-06-13

29129 new paper
2010-05-24

Today, Martin and I finally finished our paper "Approximations to the Stochastic Burgers Equation". A preprint can be downloaded below, comments are very welcome.

• M. Hairer and J. Voss: Approximations to the Stochastic Burgers Equation. Submitted, 2010.
  preprint, more…

95472 flouridation of drinking water
2010-04-29

It is of course well known that water fluoridation is a Communist conspiracy to sap and impurify all of our precious bodily fluids. Still, I am surprised to learn that one of the political parties running in the UK's upcoming general elections uses their opposition to water fluoridation as a campaign topic.

Can you guess which party this is? (for the answer click here)

15289 Sampling Conditioned Hypoelliptic Diffusions
2010-04-23

Only one day after we submitted the revised version of our paper Sampling Conditioned Hypoelliptic Diffusions (see my previous blog post), the article was accepted! It will appear in the Annals of Applied Probability.

• M. Hairer, A.M. Stuart and J. Voss: Sampling Conditioned Hypoelliptic Diffusions. To appear in the Annals of Applied Probability, 2010.
  preprint, more…

64681 updated paper
2010-04-20

In order to address the referee's comments, we have prepared an updated version the following article:

• M. Hairer, A.M. Stuart and J. Voss: Sampling Conditioned Hypoelliptic Diffusions. To appear in the Annals of Applied Probability, 2010.
  preprint, more…

78270 Talk at Maths2010
2010-04-13

I put up the slides from my talk at the Maths2010 conference in Edinburgh. Since I had only 15 minutes, the talk is nearly free of contents, but in compensation there are many nice pictures. I'm particularly fond of the torus on page 8 (which was surprisingly difficult to generate).

Older entries can be found on the next page …

Copyright © 2010, Jochen Voss. All content on this website (including text, pictures, and any other original works), unless otherwise noted, is licensed under a Creative Commons Attribution-Share Alike 3.0 License.