assemble_pdb_structures
Merge separate PDB files into a single structure, recombining processed components or building multi-chain complexes for downstream modeling.
Instructions
Merge multiple PDB files into a single PDB file.
WHEN TO USE
Use after split_pdb + fix_pdb_structure when you have separately processed components (e.g. fixed protein + original ligand) that need to be recombined before relaxation. Also useful for building hetero-complexes from individual chain files.
WORKFLOW POSITION
Optional step between fix_pdb_structure and relax_pdb_structure.
DECISION GUIDANCE
chain_id_map: Always provide this if you have performed split → fix → assemble, because fix_pdb_structure may have altered chain IDs. Map by the basename of the input file (e.g. {"protein_A_fixed.pdb": "A"}).
handle_conflicts (default "rename"): Use "rename" (default) for most cases — it is safe and non-destructive. Use "merge" only when two files represent the same biological chain split across files (e.g. modelled N-terminal extension + crystal structure). Never use "error" in automated workflows.
renumber_residues (default False): Only set True if downstream tools require sequential numbering from 1. Renumbering loses the original residue IDs, which makes cross-referencing with the source PDB harder.
renumber_atoms (default False): Set True if the output PDB will be read by tools that expect strictly sequential atom serials.
OUTPUT — WHAT TO CHECK
Run query_pdb_structure on the assembled output to verify chain IDs, residue counts, and that no unexpected gaps were introduced by the merge.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| notes | No | Record which components are being merged and why, e.g. "re-assembling fixed chain A with original ligand files before relaxation". | |
| input_pdbs | Yes | Ordered list of PDB paths to merge (order determines chain order in the output). | |
| output_pdb | Yes | Path for the assembled output file. | |
| chain_id_map | No | Map of input basename → desired output chain ID. | |
| renumber_atoms | No | Renumber all atom serials sequentially (default False). | |
| handle_conflicts | No | "rename" | "merge" | "error" (default "rename"). | rename |
| renumber_residues | No | Renumber residues in every chain from 1 (default False). |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |