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    Ivy Biosciences Docs/Tools/Databases/Biotite/Structure workflows

    Structure workflows

    Load PDB and mmCIF with Biotite, superpose for RMSD, split chains into per-chain PDB files, and export mmCIF — stripping waters and ligands first.

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    Structure workflows let you load PDB and mmCIF files, superpose structures to measure RMSD, and extract chains for export. Stripping waters and ligands and normalizing alternate locations before superposition are what most affect whether your RMSD reflects the atoms you actually care about.

    Where this code runs

    You cannot open a shell on the platform yourself. The scripts on this page are plain Biotite Python and shell: ask Ivy in chat to run them in the chat's code workspace, which ships Biotite, or run them on your own machine.

    Load and inspect structures

    from biotite.structure.io import load_structure

structure = load_structure("inputs/structures/1crn.pdb")
print("Atoms:", structure.array_length())
print("Chains:", structure.get_chain_count())
print("Residues:", structure.res_id[-1])

    Center and superpose

    import biotite.structure as struc

mobile = load_structure("inputs/structures/mobile.pdb")
target = load_structure("inputs/structures/reference.pdb")

transform = struc.fit_superposition(mobile, target)
mobile_aligned = struc.apply_translation(
    struc.apply_rotation(mobile, transform.rotation), transform.translation
)

print("RMSD:", struc.rmsd(target, mobile_aligned))
mobile_aligned.write("outputs/mobile_aligned.pdb")

    Extract chains and save

    from biotite.structure.io.pdb import PDBFile

pdb = PDBFile.read("inputs/structures/complex.pdb")
structure = pdb.get_structure()

chains = structure.get_unique_chains()
for chain_id in chains:
    chain = structure[structure.chain_id == chain_id]
    out = PDBFile()
    out.set_structure(chain)
    out.write(f"outputs/chain_{chain_id}.pdb")

    Common tips

    • Normalize alternate locations and occupancy before superposition.
    • Remove water/ligands if you only need backbone atoms for RMSD.
    • When exporting to mmCIF, keep atom ordering stable to ease downstream diffing.

    Minimal export to mmCIF

    from biotite.structure.io.mmtf import MMTFFile
from biotite.structure.io.mmcif import MMCIFFile

mmtf = MMTFFile.read("inputs/structures/model.mmtf")
structure = mmtf.get_structure()

mmcif = MMCIFFile()
mmcif.set_structure(structure)
mmcif.write("outputs/model.cif")

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    Sequence analysis guide

    Parse FASTA and GenBank with Biotite, read GC content, run pairwise and multiple alignments over a substitution matrix, and write a consensus FASTA.

    Troubleshooting Biotite

    Fix missing DSSP or OpenMM, FASTA and GenBank parse errors, out-of-memory batches, and RMSD spikes from unmatched chain IDs — and when to retry instead.

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