Analysis using MDAnalysis 1.0
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Run on GalaxyAnalysis of MD trajectories using MDAnalysis, generating a Ramachandran plot and various timeseries.
Associated Tutorial
This workflows is part of the tutorial Analysis of molecular dynamics simulations, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Chris Barnett
Tutorial Author(s): Christopher Barnett, Tharindu Senapathi, Simon Bray, Nadia Goué
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| DCD input | #main/DCD input | DCD input |
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| PDB input | #main/PDB input | PDB input |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | RDF Analysis | toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_rdf/mdanalysis_rdf/0.19 |
| 3 | Cosine Content | toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis/0.19 |
| 4 | Ramachandran Plots | toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_ramachandran_plot/mdanalysis_ramachandran_plot/0.1.3 |
| 5 | Distance Analysis | toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_distance/mdanalysis_distance/0.19 |
| 6 | Dihedral Analysis | toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_dihedral/mdanalysis_dihedral/0.19 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Cosine Content plot | #main/Cosine Content plot | n/a |
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| Cosine Content raw data | #main/Cosine Content raw data | n/a |
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| Dihedral Analysis plot | #main/Dihedral Analysis plot | n/a |
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| Dihedral Analysis raw data | #main/Dihedral Analysis raw data | n/a |
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| Distance Analysis plot | #main/Distance Analysis plot | n/a |
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| Distance Analysis raw data | #main/Distance Analysis raw data | n/a |
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| RDF Analysis plot | #main/RDF Analysis plot | n/a |
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| RDF Analysis raw data | #main/RDF Analysis raw data | n/a |
|
| Ramachandran Plot | #main/Ramachandran Plot | n/a |
|
| Ramachandran Plot raw data | #main/Ramachandran Plot raw data | n/a |
|
Version History
master
Creators and Submitter
Views: 1566 Downloads: 210 Runs: 0
Created: 2nd Jun 2025 at 11:04
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
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