Difference between revisions of "Fabry:Normal mode analysis/Journal"
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Rackersederj (talk | contribs) (→Atomic Displacement Analysis) |
Staniewski (talk | contribs) (→Atomic Displacement Analysis and Correlation Matrix) |
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=== Atomic Displacement Analysis and Correlation Matrix === |
=== 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. |
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 atomic_displacement.R] |
+ | Rscript [https://dl.dropbox.com/u/13796643/fabry/NMA/scripts/atomic_displacement.R.html atomic_displacement.R] |
| − | Rscript [https://dl.dropbox.com/u/13796643/fabry/NMA/scripts/corrMatrix.R corrMatrix.R] |
+ | 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 |
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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
