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ChopChopMF: Overview

ChopChopMF is a ChimeraX plug-in that wraps a lot of the manual, error-prone work of analyzing AlphaFold/ColabFold models — cropping, coloring by confidence, mapping AlphaMissense scores, reading PAE plots, running interface analysis, searching for structural homologs — into a point-and-click GUI. It does not replace ChimeraX; it drives it. Every button click is really just a ChimeraX command being run for you.

Beginner: why this matters

If you already have an AlphaFold or ColabFold model open in ChimeraX, ChopChopMF is usually the fastest way to answer the three questions you'll ask about almost every prediction:

  1. Which parts of this model can I trust? → pLDDT coloring, PAE contacts
  2. Is this residue/domain conserved, and does it carry a known disease-relevant variant? → Sequence alignment, AlphaMissense fetch/mapping
  3. What does this structure interact with, and where? → PDBePISA interface analysis, Foldseek homolog search

This section of the guide is organized by task, not by button — see Workflows & Tips for step-by-step recipes that combine ChopChopMF tools with the concepts explained earlier in this guide (pLDDT, PAE, AlphaMissense).

Installation

Beginner: requirements

ChopChopMF needs ChimeraX ≥ 1.9 — download ChimeraX here first if you don't have it.

  1. In ChimeraX, go to Tools → More Tools — this opens the Toolshed browser.
  2. Search for ChopChopMF and install the latest version.
  3. If it isn't listed directly on the Toolshed start page, just search for it by name.

No command-line knowledge needed — this is the recommended path for most users.

In the ChimeraX command line:

toolshed reload all
toolshed install ChopChopMF

Relaunch ChimeraX after installation.

  1. Download the latest ChopChopMF wheel file from the releases page.
  2. In ChimeraX, run: 
    toolshed install chimerax_chopchopmf-1.3-py3-none-any.whl
  3. Relaunch ChimeraX.

Once installed, ChopChopMF adds its own tab inside ChimeraX — no further command-line usage is required afterwards.

What ChopChopMF can do — at a glance

Category Tools Typical use case
Alignment Sequence Alignment, Missense Alignment Conservation coloring; mapping human AlphaMissense scores onto orthologs
Fetch PDB AlphaMissense DB fetch, AlphaFold2 fetch/search/predict Pull structures + per-residue annotation without leaving ChimeraX
Modify Structure Crop, Delete Chain, Duplicate, Measure Center, Symmetry Copies Cleaning up models before downstream analysis (e.g. Foldseek)
Analyze Structure PAE Contacts, PAE Interaction Residues, PDBePISA interface scoring, ΔG solvation analysis, Foldseek search Multimer/complex confidence and interface characterization
Undo One-click ChimeraX undo shortcut Note: does not undo Crop or Delete Chain

Destructive operations

Crop Structure and Delete Chain are terminal — they cannot be undone via ChimeraX's normal undo, and ChopChopMF's own Undo shortcut does not cover them either. Use Duplicate Structure first if you want to keep an untouched copy, and use "Hide Deletion Preview" in Crop to check your residue range before committing.

Supported file formats

Format Purpose Notes
.pdb Coordinates Column-based; can struggle with very large structures
.cif / .mmCIF Coordinates No atom/chain limits; the default format from AlphaFold/ColabFold
.mrc / .map Cryo-EM density volumes Needed for Measure Center / Symmetry Copies
.json AlphaFold PAE / confidence metadata Required alongside the .cif for PAE Contacts analysis
.defattr Per-residue attribute values Output of alignment/scoring tools; can be re-applied without recomputation
.xml PDBePISA interface data Exported manually from the PDBePISA web server
.tsv Custom AlphaMissense scores For organisms/proteins not in the default AlphaMissense DB pull

Continue to Workflows & Tips →