Download reposity and maintain structure ChimeraX-PAEVisualization/ ├── bundle_info.xml └── src/ ├── init.py └── pae_visualization.py (your main code)

Extract Fold if downloaded as zip file

Open ChimeraX 1.10 or greater

type into the command line: devel build path\to\ChimeraX-PAEVisualization toolshed install path\to\distrubtion\ChimeraX_PAEVisualization-1.0-py3-none-any.whl

The last line of the log after running the build command will give the destination of the wheel file (.whl)

If the install fails or changes/updates need to be made, run: toolshed unistall PAEVisualization devel clean path\to\ChimeraX-PAEVisualization

Then, restart chimeraX before reinstalling.

Can also be installed from zip file using toolshed installer, however this sometimes fails.

""" Create pseudobonds visualizing PAE pairs between residues.

Parameters
----------
session : chimerax.core.session.Session
    The ChimeraX session
models : list
    List of atomic structure models
file : str
    Path to AlphaFold PAE JSON file
cutoff : float, optional
    Maximum PAE value for creating pseudobonds
percentile : float, optional
    Alternative to cutoff: show interactions in bottom N percentile (0-100)
color_by_pae : bool
    If True, color pseudobonds by PAE value (green=low, red=high)
radius : float
    Base radius of pseudobonds
name : str
    Name for the pseudobond group
max_distance : float, optional
    Maximum spatial distance (Angstroms) between residues to create bond
chain_filter : str, optional
    Filter interactions: "intra" (same chain), "inter" (different chains),
    or comma-separated chain IDs like "A,B" or "A-A,B-B" for specific pairs
min_plddt : float, optional
    Minimum pLDDT score for both residues (0-100)
style : str
    Bond style: "solid", "dashed", or "by_range" (dashed for high PAE)
thickness_by_confidence : bool
    If True, make radius inversely proportional to PAE value
cache_pae : bool
    If True, cache PAE data for reuse with different parameters (uses more memory)
norm : str
    Color normalization method: "range" (min to max) or "mean" (mean ± std dev)
    Default: "range"

"""

Select all residues that participate in PAE pair pseudobonds.

Parameters
----------
session : chimerax.core.session.Session
    The ChimeraX session
pb_group_name : str, optional
    Name of the pseudobond group created by 'pae-visualization'
    Default: "PAE Pairs"
clear : bool, optional
    If True, clear existing selection first; otherwise add to it
    Default: True
chunk_size : int, optional
    Number of serial numbers per chunk for fallback selection method
    (keeps command length manageable)
    Default: 300
    
Returns
-------
residues : Residues
    The selected residues

"""

 Clear the cached PAE data to free memory.

Parameters
----------
session : chimerax.core.session.Session
    The ChimeraX session
"""