Difference between revisions of "Fabry:Normal mode analysis/Journal"
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Rackersederj (talk | contribs) (→Atomic Displacement Analysis) |
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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 atomic_displacement.R] |
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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 corrMatrix.R] |
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| + | |||
| + | |||
| + | == ElNémo == |
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| + | <!-- |
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| + | reini |
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| + | bg_color white |
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| + | |||
| + | load 120709155226319.7.pdb, 3HG3.mode7 |
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| + | dss 3HG3.mode7 |
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| + | show_as cartoon, 3HG3.mode7 |
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| + | color cyan, 3HG3.mode7 |
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| + | sele A, chain A and resi 203-207 |
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| + | color red, A |
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| + | sele B, chain B and resi 203-207 |
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| + | color red, B |
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| + | zoom |
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| + | set ray_trace, 1 |
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| + | mpng mode7CART |
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| + | |||
| + | zoom |
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| + | show_as surface,3HG3.mode7 |
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| + | set solvent_radius, 1.6 |
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| + | mpng mode7SURF |
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| + | |||
| + | delete 3HG3.mode7 |
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| + | --> |
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Revision as of 12:55, 11 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
