Convert PDB to Markdown.
Drop a Protein Data Bank file and get a clean Markdown summary in seconds. It runs entirely in your browser, so your file never leaves your device.
Drag & drop your files
or
Optimize for AI & RAG
Extra cleanup for LLM ingestion: strip HTML, fix smart quotes, tidy Unicode and spacing.
Add YAML front matter
Prepend a metadata block (title, source, date, word & token counts) for knowledge bases and RAG.
Add table of contents
Build a linked index from the headings. Handy for long documents.
Export RAG chunks (.json)
Split the result into retrieval-ready chunks. Download per file from the result panel.
Most converters quietly upload your documents to a server. This one physically can't.
Coordinates,
not a summary.
A PDB file stores a molecule as thousands of fixed-column ATOM and HETATM lines. Reading it means scanning past page after page of raw coordinates. Converting pulls out the title and the atom and chain counts.
TITLE HEMOGLOBIN
ATOM 1 N VAL A 1 6.204 16.869 4.854
ATOM 2 CA VAL A 1 6.913 17.759 4.000
HETATM 1234 O HOH B 201 10.100 20.200 30.300
# Molecular structure (PDB)
- **Title:** HEMOGLOBIN
- **Atoms:** 3
- **Chains:** 1
Everything you
actually need.
Protein Data Bank files in, a clean Markdown summary out, with no server and no account anywhere.
It never leaves your browser
Your .pdb is read and parsed on your device. Nothing is uploaded to any server, ever.
# Heading
- point one
3 chunks
AI & RAG ready
Optional cleanup, YAML front matter, a table of contents and RAG chunk export.
Works offline
Once the page has loaded you can switch off your connection and it keeps converting.
- Atoms: 3
- Chains: 1
Structure, summarised
The structure title plus the count of atoms and chains, read straight from the records.
Unicode safe
Accents, symbols and non-Latin scripts come through intact as UTF-8.
Free, and unlimited
No sign-up, no quotas, no watermarks. Convert one file or a thousand; it all runs the same way, on your own device.
What the summary
keeps.
Honest about what comes through, and what doesn't. These are the same notes the Formats list shows for PDB, so the page never drifts from what the converter really does.
Kept
3- The structure title
- The atom count
- The chain count
Dropped
2- Atom coordinates
- All other records
ATOM 1 N VAL A 1 6.204 16.869 4.854
ATOM 2 CA VAL A 1 6.913 17.759 4.000
HETATM 1234 O HOH B 201
HELIX SHEET CONECT
PDB questions,
answered.
Everything worth knowing before you drop in a structure file.
Other converters.
Working with more than structure files? These convert the same way: privately, in your browser.
FASTA to Markdown
.fasta · .fa
Biological sequence data.
FASTQ to Markdown
.fastq · .fq
Sequencing reads with quality.
GenBank to Markdown
.gb · .gbk
Annotated DNA sequences.
Newick to Markdown
.nwk · .tree
Phylogenetic trees.
GFF / GTF / BED to Markdown
.gff · .gtf · .bed
Genome feature annotations.
SAM to Markdown
.sam
Sequence alignment data.
MOL / SDF to Markdown
.mol · .sdf
Chemical structure files.
SMILES to Markdown
.smiles
Molecular structure strings.