Visualization Tools — and Why This Guide Uses ChimeraX¶
A predicted structure is a set of atomic coordinates plus confidence metadata — you need dedicated software to actually look at it, color it by pLDDT/AlphaMissense, measure distances, or produce a figure. This page gives a quick landscape of the main options, then explains (openly, as an opinion) why the rest of this guide standardizes on one of them.
The main options¶
Beginner
| Tool | License | Known for |
|---|---|---|
| ChimeraX | Free for academic/non-profit use; commercial use needs a paid UCSF license | Broad, modern feature set — cryo-EM density maps/fitting, AlphaFold/PAE integration, a large plugin ecosystem (Toolshed) |
| PyMOL | Free open-source edition; "Incentive PyMOL" (Schrödinger) is a paid, fully-supported version | The long-standing gold standard for ray-traced, publication-quality figures; deep Python scripting |
| VMD | Free for non-commercial/academic research | Strong for molecular dynamics trajectory visualization and analysis |
| Mol* | Fully open-source, free | Runs in the browser — no install; this is what powers the RCSB PDB and AlphaFold DB's own online viewers |
None of these is objectively "best" — they overlap heavily and each has a real community behind it. What matters is picking one and learning it well enough to trust what you're seeing.
Our take — and why this guide picks ChimeraX¶
This is an opinion, not a fact — taste is genuinely subjective here
This guide works exclusively with ChimeraX, for three reasons, roughly in order of how objective they are:
- It's free for the academic/non-profit use this guide is written for. (If your use is commercial, check UCSF's licensing terms before assuming that holds for you.)
- It has a large, active plugin ecosystem via the built-in Toolshed — including ChopChopMF, which this guide leans on heavily for AlphaFold-specific analysis (pLDDT/PAE/AlphaMissense coloring, Foldseek, PDBePISA) without writing a single command.
- In our (admittedly biased) opinion, it makes the best-looking figures of the options above, once you learn its rendering and lighting presets — but this is genuinely a matter of taste, and plenty of excellent structural biologists would tell you PyMOL is the real gold standard for publication-quality ray-traced images, with a scripting ecosystem that's been refined for over two decades. If you already have a PyMOL workflow you're happy with, there's no strong reason to switch on our say-so.
The one practical (non-opinion) constraint: since ChopChopMF — the tool this guide's hands-on workflows are built around — is a ChimeraX plugin, following those specific workflows does require ChimeraX. The underlying concepts (reading pLDDT/PAE, cropping a domain before a homology search, mapping interface residues) transfer to any of the tools above; only the exact button clicks are ChimeraX/ChopChopMF-specific.
Finding plugins: the ChimeraX Toolshed¶
Beginner
The ChimeraX Toolshed is ChimeraX's built-in plugin repository — browsable by category on the web, or directly inside the app via Tools → More Tools. Anyone can publish a bundle there; each listing shows a thumbnail, download counts, and ratings. It's the same mechanism the ChopChopMF installation steps use.
Two plugins this guide relies on¶
ChopChopMF
The point-and-click AlphaFold/ColabFold analysis toolkit this guide's hands-on workflows are built around: pLDDT/PAE/AlphaMissense coloring, cropping, Foldseek, PDBePISA — all covered in ChopChopMF.
FigureStyle
The last step after analysis: define lighting, per-secondary-structure cartoon style, coloring (including AlphaFold pLDDT), and export settings once as a named template — then apply it to any structure with one click. Built for easy, repeatable figures: the same template gives every structure in a paper identical, reproducible styling instead of retyping commands each time.
Advanced: what FigureStyle actually saves you
Six coloring modes (none, single color, by-chain rainbow, by B-factor, by heteroatom, AlphaFold pLDDT), configurable image export (PNG/TIFF/JPEG, custom resolution and supersampling — PNG/TIFF keep transparency, JPEG doesn't), and templates that export as JSON or standalone .cxc ChimeraX scripts for sharing with a lab or co-authors. Once a template exists, applying it from the command line is one line: figurestyle apply "Template Name" — useful for batch-rendering many structures with identical, reproducible styling (exactly the kind of consistency the best-practices page recommends for a paper's figures).
Continue to ChopChopMF →