Molecular Biology 2011

Week 0: Spectroscopy

The "Intoduction to Spectroscopy" is a revision of the lecture I started giving in last year.

slides for introduction to spectroscopyspectroscopy.pdf size: 2.9MB; md5sum: 8155b85a2fc93f15d0814b869767f6cd

Macromolecular Crystallography

These are the (preliminary) lecture notes for the course.

  1. Day 1: Crystals and X-ray Diffraction
  2. 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.
  3. Day 3: Phasing, Model Building, and Refinement
  4. 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

Last modified: Mon Nov 21, 2011 06:15PM