Difference between revisions of "Fabry:Normal mode analysis/Journal"
From Bioinformatikpedia
Rackersederj (talk | contribs) (→WEBnm@) |
Rackersederj (talk | contribs) (→ElNémo) |
||
| Line 50: | Line 50: | ||
== ElNémo == |
== 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 [https://dl.dropbox.com/u/13796643/fabry/NMA/scripts/modes.py modes.py]. From these pictures we made a movie: |
||
| − | <!-- |
||
| + | convert -delay 30 modeXSURF00* modeXSURF.gif |
||
| − | reini |
||
| − | bg_color white |
||
| − | |||
| − | load 120709155226319.7.pdb, 3HG3.mode7 |
||
| − | dss 3HG3.mode7 |
||
| − | show_as cartoon, 3HG3.mode7 |
||
| − | color cyan, 3HG3.mode7 |
||
| − | sele A, chain A and resi 203-207 |
||
| − | color red, A |
||
| − | sele B, chain B and resi 203-207 |
||
| − | color red, B |
||
| − | zoom |
||
| − | set ray_trace, 1 |
||
| − | mpng mode7CART |
||
| − | |||
| − | zoom |
||
| − | show_as surface,3HG3.mode7 |
||
| − | set solvent_radius, 1.6 |
||
| − | mpng mode7SURF |
||
| − | |||
| − | delete 3HG3.mode7 |
||
| − | --> |
||
Revision as of 09:36, 12 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
