DSeiferth/PoreFinding_pdb

Try out this protoype on HugginFace without installing anything

What does this package add?

• —Pore finding with new features:
• —Capture pore asymmetry.
• —Asymmetry of crystal/cryoEM structures due to heterogeneous subunit composition.
• —from crystal structure broken in simulations.
• —Making a tool accessible without installation or download of any package.

Path finding with ellipsoidal probe particle

1. 1.Align principal axis to z-axis
2. 2.Load HOLE output file with positions and radii of probes.
3. 3.Loop through all spherical probe particles: a) Ellipsoid initialized with spherical probe particle parameters from HOLE output. b) First Nelder-Mead 4-dim optimization to insert ellipsoid with smaller bounds for parameters [x, y, r1, θ ]. c) Second optimization with larger boundaries for parameters to further increase ellipsoid. The loop takes around 60s to complete...

Conent and Usage of (zipped) HOLE output files

example: pdbname = '7tu9aligned_z.pdb'

• —pdb files
• —pdb_name: uploaded pdb file (aligned to z-axis)
• —pdbname + 'circle.pdb': point cloud for pore surface
• —vmd files
• —pdb_name + ".vmd": vmd surface for uploaded pdb file
• —"visualisepathwayhole.tcl": vmd script for plotting the pore surface; the script can be used in the following way: "vmd -e visualisepathwayhole.tcl -args 7tu9alignedz.pdb 7tu9alignedz.vmd"
• —other files
• —"holepathwayprofile.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
• —"holepathwayprofile."+fig_format: pathway profile figure in desired format

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

example: pdbname = 7tu9aligned_z

• —vmd files
• —pdbname+'.pdbpathway_ellipse.vmd'
• —"visualisepathwayhole.tcl"
• —the script can be used in the following way: "vmd -e visualisepathwayhole.tcl -args 7tu9alignedz.pdb 7tu9alignedz.pdbpathwayellipse.vmd.vmd"
• —pdb files
• —pdbname + '.pdbellipsoid.pdb'
• —pdb_name+'.pdb'
• —other files
• —"README.md"
• —pdbname + '.pdbpathway_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

Notes

Hugging Face Spaces work as git repositories. To keep everything on GitHub but publish on Hugging Face, add the Hugging Face Space repository as a remote repository:

git remote add hf https://huggingface.co/spaces/DSeiferth/PoreFinding_pdb

Acknowledgements

• —Rocco Meli