Molecular Biology 2011
Week 0: Spectroscopy
The "Intoduction to Spectroscopy" is a revision of the lecture I started giving in last year.
Macromolecular Crystallography
These are the (preliminary) lecture notes for the course.
- Day 1: Crystals and X-ray Diffraction
- Day 2: Space Groups, Data Integration, and the Phase Problem. The rotation of the reciprocal lattice through the Ewald sphere as the crystal rotates during data collection is shown in this movie. The grey translucent sphere shows the resolution limit of the crystal. If it is greater than the Ewald sphere, the wavelength limits the data resolution, otherwise the crystal quality does.
- Day 3: Phasing, Model Building, and Refinement
- Day 4: Validation
Technical note: making waves with gnuplot
The movie of the spherical wave on the fourth slide only plays on my laptop, you can download it from here if you want to watch it. It was created using the following gnuplot script:
spherical_wave.plot
unset surf
set pm3d
set isos 500
set hidden3d
set palette rgbformulae 23,28,3
unset xtics
unset ytics
unset ztics
unset border
unset colorbox
filename = sprintf("wave%04.1f.png", t)
set output filename
#A(x,y) = A0*0.5*(1+ x**2/(x**2+y**2))
A(x,y) = A0
w(x,y) = A(x,y) *cos(k1*sqrt(x**2+y**2) - w*t)
#splot sin(k1*x+k2*y - w*t) w pm3d
splot [-20:10] [-20:10] [-10:10] w(x,y) noti
t=t+0.1
if(t<3*2*pi) reread
The script is called from the following bash script:
#!/bin/bash
rm -f wave*.png
gnuplot -e "t=0; k1=1; w=1;A0=4;set term png size 1024,800;"
spherical_wave.plot
mencoder mf://wave*.png -o spherical_wave.avi -ovc lavc -lavcopts
vcodec=mpeg4:vbitrate=9000
cp wave00.0.png ../spherical_wave.png
rm -f wave*.png
Tim Grüne