Interactive webservice (no installation needed)

You can try out the package without installing anything using a interactive web-service hosted on a webserver of the Department of Biochemistry (University of Oxford).

Output to download

Conent and Usage of (zipped) HOLE output files

example: pdb_name = ‘7tu9_aligned_z.pdb’ - pdb files

• pdb_name: uploaded pdb file (aligned to z-axis)

• pdb_name + ‘_circle.pdb’: point cloud for pore surface

• vmd files - pdb_name + “.vmd”: vmd surface for uploaded pdb file - “visualise_pathway_hole.tcl”: vmd script for plotting the pore surface; the script can be used in the following way: “vmd -e visualise_pathway_hole.tcl -args 7tu9_aligned_z.pdb 7tu9_aligned_z.vmd”

• chimera files - chimera_pore.py : you have to adjust the path and the filenames as discussed here - chimeraX_pore.py

• pymol_pore_visu.py

• other files - “hole_pathway_profile.csv”: A DataFrame containing the results of the hole analysis, with the following columns:

  • ‘Label z [A]’: the z-coordinate of each point along the pore axis.

  • ‘Label Radius [A]’: the radius of the pore at each point.

  • ‘Label’ corresponds to the labels provided in the labels parameter in the hole_analysis.analysis() function.

  • “README.md”

  • “hole.out”: HOLE output

  • “hole_pathway_profile.”+fig_format: pathway profile figure in desired format

Conent and Usage of (zipped) output files for pathfinding with an ellipsoidal probe particle

example: pdb_name = 7tu9_aligned_z - vmd files

• pdb_name+’.pdb_pathway_ellipse.vmd’

• “visualise_pathway_hole.tcl”

• the script can be used in the following way: “vmd -e visualise_pathway_hole.tcl -args 7tu9_aligned_z.pdb 7tu9_aligned_z.pdb_pathway_ellipse.vmd.vmd”

• chimera files - chimera_pore.py : you have to adjust the path and the filenames as discussed `here <https://porefinding.readthedocs.i> - chimeraX_pore.py

• pymol_pore_visu.py

• pdb files - pdb_name + ‘.pdb_ellipsoid.pdb’ - pdb_name+’.pdb’

• other files - “README.md” - pdb_name + ‘.pdb_pathway_ellipse.txt’: A DataFrame containing the results of the pathfinding analysis, with the following columns:

  • “x”, “y”, “z”: position of ellipsoid center

  • “a”, “b”: larger and smaller radius of the ellipsoid

  • “theta”: orientation of ellipsoid

  • figure plotting the spherical HOLE radius and the larger radius of the ellipsoid