Convert PDB structures to CIF or mmCIF while preserving annotations and multi-model assemblies. Learn more
Convert PDB structures to CIF or mmCIF while preserving annotations and multi-model assemblies. Learn more
Convert PDB structures to CIF or mmCIF while preserving annotations and multi-model assemblies. Learn more
Convert Protein Data Bank files to FASTA sequence format
Convert Protein Data Bank files to MOL2 molecular format
Convert CSV and TSV files containing sequence data to FASTA format with flexible column mapping and automatic delimiter detection
Translate DNA sequences to protein sequences using genetic code
Convert single-letter amino acid codes to three-letter codes
Reverse translate protein sequences to possible DNA sequences
Convert three-letter amino acid codes to single-letter codes
Convert TXT or plain text sequences into FASTA format files for DNA, RNA, and protein workflows with cleanup, validation, and downloads
Extract sequence features (CDS, mRNA, gene, etc.) from GenBank files in FASTA format with support for spliced features
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
Convert Protein Data Bank files to FASTA sequence format
Convert Protein Data Bank files to MOL2 molecular format
Convert CSV and TSV files containing sequence data to FASTA format with flexible column mapping and automatic delimiter detection
Translate DNA sequences to protein sequences using genetic code
Convert single-letter amino acid codes to three-letter codes
Reverse translate protein sequences to possible DNA sequences
Convert three-letter amino acid codes to single-letter codes
Convert TXT or plain text sequences into FASTA format files for DNA, RNA, and protein workflows with cleanup, validation, and downloads
Extract sequence features (CDS, mRNA, gene, etc.) from GenBank files in FASTA format with support for spliced features
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
Configure inputs to begin
Set options on the left, then click “Convert”.
PDB to CIF Converter transforms protein structure files from the legacy PDB format into PDBx/mmCIF (macromolecular Crystallographic Information File) format. The PDB format, introduced in the 1970s, uses fixed-width columns inherited from punched-card computing, which imposes hard limits: a maximum of 99,999 atoms and 62 chains per file. The mmCIF format removes these constraints entirely, supporting unlimited atoms, residues, and chains in a single file.
The worldwide Protein Data Bank (wwPDB) has designated PDBx/mmCIF as the standard format for deposition, annotation, and archiving. As the PDB archive approaches the exhaustion of its four-character accession codes (expected before 2028), new entries with extended 12-character PDB IDs will only be available in mmCIF format. Software tools and pipelines that still depend on the legacy PDB format will need to transition to mmCIF by 2029.
Beyond removing size constraints, mmCIF offers several practical advantages. Its tabular, tag-value structure is easier to parse programmatically than the PDB positional column format. It carries richer metadata, including detailed experimental conditions, refinement statistics, and chemical component descriptions that the legacy format cannot represent. These properties make mmCIF the preferred input for modern structural biology software, molecular dynamics packages, and deposition workflows.
ProteinIQ provides browser-based PDB to CIF conversion with no software installation or account required. The conversion runs entirely client-side, so structure data never leaves the browser.
| Input | Description |
|---|---|
input | A protein structure in PDB format. Accepts pasted PDB content, uploaded .pdb or .ent files (up to 50 MB), or a PDB ID fetched directly from RCSB (e.g., 1CRN). |
All settings are found under Conversion options.
| Setting | Type | Default | Description |
|---|---|---|---|
Preserve secondary structure | Toggle | On | Includes secondary structure annotations (helices, sheets) in the CIF output. |
Include HETATM records | Toggle | On | Retains heteroatom records such as ligands, water molecules, and ions. |
Preserve temperature factors | Toggle | On | Carries over B-factor (temperature factor) values for each atom. |
Include all models | Toggle | Off | Converts all models in multi-model PDB files (e.g., NMR ensembles). When off, only the first model is converted. |
The converter produces a single mmCIF-formatted text output that can be copied to the clipboard or downloaded as a file.