Research Data Leeds Repository

Citation

Welch, Robert (2020) All-atom Ndc80C trajectories, KOBRA parameterisation and validation. University of Leeds. [Dataset] https://doi.org/10.5518/760

Dataset description

Raw data and Python scripts that generate the plots seen in 'KOBRA: A Fluctuating Elastic Rod Model for Slender Biological Macromolecules'. The MD trajectories are in the AMBER format. For KOBRA trajectories, download FFEA from ffea.bitbucket.io. The python scripts are mixed between Python 2.x and python 3.x. MDAnaysis, ISAMBARD, SCWRL4, PyMOL, VMD and PyPCAZip are recommended.

Keywords:	FFEA, Molecular Dynamics, AMBER, KOBRA, Simulation Trajectories
Subjects:	C000 - Biological sciences > C700 - Molecular biology, biophysics & biochemistry > C790 - Molecular biology, biophysics & biochemistry not elsewhere classified
Divisions:	Faculty of Engineering and Physical Sciences > School of Physics and Astronomy
Related resources:	Location Type https://doi.org/10.1039/D0SM00491J Publication https://eprints.whiterose.ac.uk/163324/ Publication https://bitbucket.org/Robert-Welch/kobra-raw-data/src/master/ Software
Date deposited:	09 Aug 2020 20:08
URI:	https://archive.researchdata.leeds.ac.uk/id/eprint/725
Additional details Additional details Creators or authors: Creators ORCID Other ID Email Primary affiliation Primary affiliation ID Primary affiliation ID type Secondary affiliation Secondary affiliation ID Secondary affiliation ID type Welch, Robert https://orcid.org/0000-0002-0135-0112 University of Leeds https://ror.org/024mrxd33 ror Type of data: Dataset Research funders: William Wright Scholarship, EPSRC Grant numbers: EP/S030671/1 Publication date: 2020 Resource language: English Metadata language: English Publisher: University of Leeds Contact email: D.J.Read@leeds.ac.uk Last Modified: 30 Oct 2024 15:09

Files

Documentation

README.md [3kB] README.md [3kB] README.md [3kB] Security: Anyone File name: README.md Content type: Documentation License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 3kB

Data

B recovery iterations [175MB] B recovery iterations [175MB] B recovery iterations [175MB] Security: Anyone File name: B_recovery.zip Content type: Data Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 175MB

beta recovery iterations [53MB] beta recovery iterations [53MB] beta recovery iterations [53MB] Security: Anyone File name: recover_twist.zip Content type: Data Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 53MB

NDC80 parametrerisation source data [462MB] NDC80 parametrerisation source data [462MB] NDC80 parametrerisation source data [462MB] Security: Anyone File name: ndc80c_sims.zip Content type: Data Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 462MB

Raw data for performance evaluation [107B] Raw data for performance evaluation [107B] Raw data for performance evaluation [107B] Security: Anyone File name: scaling_openMP_arc2.csv Content type: Data Mime-Type: text/csv License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 107B

Raw data for performance evaluation [169B] Raw data for performance evaluation [169B] Raw data for performance evaluation [169B] Security: Anyone File name: scaling_single_thread_arc2.csv Content type: Data Mime-Type: text/csv License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 169B

NDC80c build [79kB] NDC80c build [79kB] NDC80c build [79kB] Security: Anyone File name: build_ndc80c.zip Content type: Data Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 79kB

AMBER trajectories [4GB] AMBER trajectories [4GB] AMBER trajectories [4GB] Security: Anyone File name: AMBER_trajectories.zip Content type: Data Mime-Type: application/zip License: Creative Commons Attribution 4.0 International (CC BY 4.0) File size: 4GB

Program

Calculate error in recovered parameters [2kB] Calculate error in recovered parameters [2kB] Calculate error in recovered parameters [2kB] Security: Anyone File name: calc_parm_err.py Content type: Program File size: 2kB

Compare bend angles (no plot) [1kB] Compare bend angles (no plot) [1kB] Compare bend angles (no plot) [1kB] Security: Anyone File name: compare_bend_angles Content type: Program File size: 1kB

Plot eigenvalues for rod vs all-atom [8kB] Plot eigenvalues for rod vs all-atom [8kB] Plot eigenvalues for rod vs all-atom [8kB] Security: Anyone File name: compare_first_modes.py Content type: Program File size: 8kB

Plot error in B [8kB] Plot error in B [8kB] Plot error in B [8kB] Security: Anyone File name: compare_recovered_eigenvalues.py Content type: Program File size: 8kB

Create continuous plot [11kB] Create continuous plot [11kB] Create continuous plot [11kB] Security: Anyone File name: continuous.py Content type: Program File size: 11kB

Create discrete plot [3kB] Create discrete plot [3kB] Create discrete plot [3kB] Security: Anyone File name: example_fig_pov.py Content type: Program File size: 3kB

Ndc80c parameter extraction script [47kB] Ndc80c parameter extraction script [47kB] Ndc80c parameter extraction script [47kB] Security: Anyone File name: ndc_extractor.py Content type: Program File size: 47kB

Create parallel transport plot [1kB] Create parallel transport plot [1kB] Create parallel transport plot [1kB] Security: Anyone File name: parallel_transport.py Content type: Program File size: 1kB

POV-ray utility script [22kB] POV-ray utility script [22kB] POV-ray utility script [22kB] Security: Anyone File name: povexport.py Content type: Program File size: 22kB

Shared FFEA python library [4kB] Shared FFEA python library [4kB] Shared FFEA python library [4kB] Security: Anyone File name: slender_analysis.py Content type: Program File size: 4kB

Shared FFEA python library [14kB] Shared FFEA python library [14kB] Shared FFEA python library [14kB] Security: Anyone File name: slender_analysis_lib.py Content type: Program File size: 14kB

Iterative closest point algorithm by Clay Flannigan [3kB] Iterative closest point algorithm by Clay Flannigan [3kB] Iterative closest point algorithm by Clay Flannigan [3kB] Security: Anyone File name: icp.py Content type: Program File size: 3kB

Matplotlib parameters for publication [816B] Matplotlib parameters for publication [816B] Matplotlib parameters for publication [816B] Security: Anyone File name: global_plot_params.py Content type: Program File size: 816B

Plot PCA heatmap [3kB] Plot PCA heatmap [3kB] Plot PCA heatmap [3kB] Security: Anyone File name: mode_plotter.py Content type: Program File size: 3kB

Plot performance and scaling graphs [2kB] Plot performance and scaling graphs [2kB] Plot performance and scaling graphs [2kB] Security: Anyone File name: performance_plotter.py Content type: Program File size: 2kB

Generate every plot [1kB] Generate every plot [1kB] Generate every plot [1kB] Security: Anyone File name: plot_all.py Content type: Program File size: 1kB

Plot the eigenvalues of B [1kB] Plot the eigenvalues of B [1kB] Plot the eigenvalues of B [1kB] Security: Anyone File name: plot_B_eigenvalues.py Content type: Program File size: 1kB

Plot the B eigenvalues for multiple iterations of the B recovery algorithm [2kB] Plot the B eigenvalues for multiple iterations of the B recovery algorithm [2kB] Plot the B eigenvalues for multiple iterations of the B recovery algorithm [2kB] Security: Anyone File name: plot_B_recovery_iterative.py Content type: Program File size: 2kB

Plot per-node RMSD [1kB] Plot per-node RMSD [1kB] Plot per-node RMSD [1kB] Security: Anyone File name: plot_rmsds.py Content type: Program File size: 1kB

Plot RMSD vs time [3kB] Plot RMSD vs time [3kB] Plot RMSD vs time [3kB] Security: Anyone File name: rmsd_convergence.py Content type: Program File size: 3kB

Plot twist recovery [4kB] Plot twist recovery [4kB] Plot twist recovery [4kB] Security: Anyone File name: twist_recovery_progressive_plot.py Content type: Program File size: 4kB

Plot hinge angle distribution [9kB] Plot hinge angle distribution [9kB] Plot hinge angle distribution [9kB] Security: Anyone File name: hinge_analysis_lib.py Content type: Program File size: 9kB