Fabry:Normal mode analysis/Journal

Fabry Disease » Normal_mode_analysis  » Journal

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Graphical representation VMD:

Coloring Method: Chain
Material: Glossy
Drawing Method: QuickSurf
Radius Scale: 0.8
Density Isovalue: 0.3
Grid Spacing: 0.5
Surface Quality: Max
Orthographic View
Color: green2
Light: 0,2,3

...rather not so good. I like pymol:

load 3HG2.png
color black, 3HG2
sele A, chain A and 3HG2 and resi 203-207
color red, A
sele B, chain B and 3HG2 and resi 203-207
color red, B
...
delete 3HG2.mode9
load 3HG2.mode10.xyz
load_traj 3HG2.mode10.dcd
show spheres, 3HG2.mode10
color cyan, 3HG2.mode10
zoom A
#click on bubbles
color red, sele
zoom B
#click on bubbles
color red, sele

zoom
show_as surface,3HG2.mode10
set solvent_radius, 1.6
mpng mode10

make a movie

convert -delay 30 *.ppm modeX.gif

Atomic Displacement Analysis and Correlation Matrix

For a better display of the two individual chains, we decided to replot the provided data.

Rscript atomic_displacement.R
Rscript corrMatrix.R

ElNémo

Make nice pictures in pymol. Again we colored the binding site and also we could assign a secondary structure. For this we used the pymol script modes.py. From these pictures we made a movie:

convert -delay 30 modeXSURF00* modeXSURF.gif