FoldSift

A lightweight protein structure viewer and curation tool for VS Code.

FoldSift lets protein designers preview molecular structures inline, cycle through a folder full of candidate designs, and triage the keepers into a CSV — without ever leaving the editor. Rendering is powered by Mol*, the same engine behind the RCSB PDB, so you get full representations, selections, measurements, and screenshot/camera controls for free.

💡 Structure files still open as plain text by default, so you can read the raw coordinates whenever you want. The 3D viewer is one right-click away.

Install

1. Install FoldSift from the VS Code Marketplace — or open the Extensions panel (Cmd/Ctrl+Shift+X), search FoldSift, and click Install.
2. Right-click a structure file (or a folder of them) in the Explorer and pick a FoldSift option:
   • FoldSift: View Structure — open one structure in the 3D viewer.
   • FoldSift: View Folder — cycle through every structure in a folder.
   • FoldSift: Curate Structures — cycle and triage keepers into a CSV.

That's it — no setup or external tools required.

Features

• 3D structure viewer — the full Mol* viewport embedded in a VS Code tab.
• Folder cycling — step through every structure in a folder with the ◀ ▶ buttons, a slider, or the ←/→ arrow keys. Files load lazily, so a folder with hundreds of designs stays light on memory.
• Curation to CSV — mark the structures you want to keep and export them, with per-structure metadata and free-text comments, to a timestamped CSV.
• Wide format support — works with the formats below straight from raw text.
• Reads as text too — view the underlying coordinates anytime; the 3D editor is opt-in, not forced.

Supported formats

Extension(s)	Format
.pdb, .ent	PDB
.pdbqt	AutoDock PDBQT
.cif, .mmcif	mmCIF
.gro	GROMACS
.mol2	Tripos MOL2
.sdf, .sd	SDF
.mol	MDL MOL
.xyz	XYZ
.bcif	BinaryCIF

Any of the above may also be gzip-compressed (e.g. model.pdb.gz, 1abc.bcif.gz) — FoldSift decompresses them transparently.

Usage

View a single structure

Right-click a structure file in the Explorer → FoldSift: View Structure. (Or use Reopen Editor With… → FoldSift Structure Viewer from an open file.)

Cycle through a folder

Right-click a folder — or multi-select several files — → FoldSift: View Folder. Use ◀ ▶, the slider, or the ←/→ arrow keys to move between structures.

Curate a set of structures

Right-click a folder → FoldSift: Curate Structures, then:

1. Click Start selection — this creates foldsift_selections_<timestamp>.csv in the folder.
2. While cycling, click Keep (or press S) to mark the current structure; click/press again to unmark.
3. Optionally type a note in the Comment box — it's saved per structure and written next to it in the CSV.
4. Click End selection to finish and open the CSV.

The CSV is rewritten atomically on every change, so unmarking a structure cleanly removes its row and comment edits land immediately.

CSV columns

Column	Description
index	1-based position in the cycled set
filename	File name
full_path	Absolute path on disk
format	Parsed format (pdb, mmcif, …)
num_chains	Chain count
num_residues	Residue count
num_atoms	Atom count
seq_length	Sequence length
sequence	One-letter sequence, chains joined by /
comment	Your free-text note for this structure
selected_at	ISO-8601 timestamp when kept

Sequence and counts are extracted for PDB-family and mmCIF inputs; coordinate-only formats (e.g. .xyz, .gro, .mol2) render in the viewer but leave those columns blank.

Settings

Setting	Default	Description
foldsift.recursiveFolderScan	false	Include structures in subfolders when scanning a folder.
foldsift.backgroundColor	#1e1e1e	Viewport background color (hex).
foldsift.keepHotkey	s	Single key used to toggle Keep during curation.

Keyboard shortcuts

Key	Action
← / →	Previous / next structure
S	Toggle Keep on the current structure (during curation)

The Keep key defaults to S and can be changed via foldsift.keepHotkey. Shortcuts are ignored while the Comment box is focused, so you can type freely.

Requirements

• VS Code 1.85.0 or newer.

Source code & contributing

FoldSift is open source (MIT). The code lives at github.com/KodyKlupt/FoldSift — issues and pull requests are welcome. To build it locally: npm install, npm run compile, then press F5 in VS Code to launch an Extension Development Host.

Credits

Developed by Kody Klupt.

3D rendering by Mol* (Sehnal et al.). FoldSift bundles Mol* and provides the VS Code integration and curation workflow.

License

Released under the MIT License © 2026 Kody Klupt.