Difference between revisions of "Fabry:Normal mode analysis/Journal"

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[[Fabry Disease]] » [[Fabry:Normal_mode_analysis | Normal_mode_analysis]] » Journal
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<hr>
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[[Category: Fabry Disease 2012]]
 
== WEBnm@ ==
  
== WEBnm@ ==
 
Graphical representation VMD:
  
Graphical representation VMD:
Line 11: Line 15:
 
Color: green2
  
Color: green2
 
Light: 0,2,3
  
Light: 0,2,3
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...rather not so good. I like pymol:
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load 3HG2.png
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color black, 3HG2
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sele A, chain A and 3HG2 and resi 203-207
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color red, A
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sele B, chain B and 3HG2 and resi 203-207
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color red, B
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...
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delete 3HG2.mode9
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load 3HG2.mode10.xyz
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load_traj 3HG2.mode10.dcd
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show spheres, 3HG2.mode10
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color cyan, 3HG2.mode10
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zoom A
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#click on bubbles
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color red, sele
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zoom B
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#click on bubbles
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color red, sele
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  +
zoom
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show_as surface,3HG2.mode10
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set solvent_radius, 1.6
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mpng mode10
   
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make a movie
 
convert -delay 30 *.ppm modeX.gif
  
convert -delay 30 *.ppm modeX.gif
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=== Atomic Displacement Analysis and Correlation Matrix ===
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For a better display of the two individual chains, we decided to replot the provided data.
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Rscript [https://dl.dropbox.com/u/13796643/fabry/NMA/scripts/atomic_displacement.R.html atomic_displacement.R]
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Rscript [https://dl.dropbox.com/u/13796643/fabry/NMA/scripts/corrMatrix.R.html corrMatrix.R]
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== ElNémo ==
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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 [https://dl.dropbox.com/u/13796643/fabry/NMA/scripts/modes.py modes.py]. From these pictures we made a movie:
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convert -delay 30 modeXSURF00* modeXSURF.gif

Latest revision as of 23:52, 16 July 2012

Fabry Disease » Normal_mode_analysis  » Journal

WEBnm@

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
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