Difference between revisions of "Task9 Hemochromatosis Protocol"
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Bernhoferm (talk | contribs) (→Structure preparation) |
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== Structure preparation == |
== Structure preparation == |
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| + | Make both structures equal (especially for WEBnm@): |
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| − | |||
'perl repairPDB.pl 1a6z.ent C: -jprot -offset 22 > 1a6zC.pdb' |
'perl repairPDB.pl 1a6z.ent C: -jprot -offset 22 > 1a6zC.pdb' |
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'perl repairPDB.pl 1de4.ent A: -jprot -offset 22 > 1de4A.pdb' |
'perl repairPDB.pl 1de4.ent A: -jprot -offset 22 > 1de4A.pdb' |
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| + | Sample PyMol script for movie generation: |
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| + | <source lang="python"> |
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| + | #start |
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| + | reinitialize |
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| + | load ../1a6zC.pdb, 1a6zC |
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| + | load ../elnemo/1a6zC/7.pdb, Mode |
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| + | |||
| + | dss |
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| + | |||
| + | hide everything, all |
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| + | show cartoon, all |
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| + | |||
| + | color green, 1a6zC |
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| + | color red, Mode |
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| + | |||
| + | mset 1 -11 -2 |
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| + | set ray_trace_frames, 1 |
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| + | </source> |
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<br style="clear:both;"> |
<br style="clear:both;"> |
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Latest revision as of 16:41, 25 July 2012
Structure preparation
Make both structures equal (especially for WEBnm@):
'perl repairPDB.pl 1a6z.ent C: -jprot -offset 22 > 1a6zC.pdb' 'perl repairPDB.pl 1de4.ent A: -jprot -offset 22 > 1de4A.pdb'
WEBnm@
Sample PyMol script for movie generation: <source lang="python">
- start
reinitialize load ../1a6zC.pdb, 1a6zC load ../webnma/modes_visualization/1a6zC.mode7.xyz, Mode load_traj ../webnma/modes_visualization/1a6zC.mode7.dcd, Mode
hide everything, all show cartoon, 1a6zC show spheres, Mode show mesh, Mode
color green, 1a6zC color red, Mode
mset 2 -10 -2 set ray_trace_frames, 1 set sphere_transparency, 0.7 </source>
ElNemo
Sample PyMol script for movie generation: <source lang="python">
- start
reinitialize load ../1a6zC.pdb, 1a6zC load ../elnemo/1a6zC/7.pdb, Mode
dss
hide everything, all show cartoon, all
color green, 1a6zC color red, Mode
mset 1 -11 -2
set ray_trace_frames, 1
</source>
