external-structures
Table of Contents
A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.
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Provided by
There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.
Required by
There are no anvi’o tools that require this artifact directly, which means it is most likely an end-product for the user.
Can be used by
anvi-gen-structure-database anvi-update-structure-database
Description
By default, anvi’o predicts protein structures (with MODELLER or ColabFold) when creating a structure-db. Yet, if the user provides an external structures file, then anvi’o does not predict anything, and instead uses this file to import pre-computed structures into the structure-db. This is handy when you already have structures, or when you predicted them with another tool (e.g. AlphaFold3).
External structures is a user-provided TAB-delimited file. Its header determines the format, and the format must match the input you are building the structure-db from (a contigs-db, or a pangenome). Anvi’o auto-detects which one you provided.
File format
From a contigs database
A two-column file mapping each gene caller id to a structure file:
| gene_callers_id | path |
|---|---|
| 1 | path/to/gene1/structure.pdb |
| 2 | path/to/gene2/structure.pdb |
| (…) | (…) |
where,
- gene_callers_id is a gene call in the contigs-db,
- path points to a protein-structure-txt for that gene.
From a pangenome
When you build the structure-db from a pangenome (a pan-db plus its genomes-storage-db), a gene is identified by the genome it comes from and its gene caller id, so the file has a genome column:
| genome_name | gene_callers_id | path |
|---|---|---|
| G_01 | 1 | path/to/structure_A.pdb |
| G_01 | 42 | path/to/structure_B.pdb |
| G_02 | 17 | path/to/structure_C.pdb |
| (…) | (…) | (…) |
where,
- genome_name is a genome in the genomes-storage-db,
- gene_callers_id is a gene call in that genome,
- path points to a protein-structure-txt for that gene.
You do not provide the gene cluster: anvi’o derives it from the pan-db for each gene. Each gene must therefore belong to a gene cluster in your pangenome.
Anvi’o will test the integrity of each file, and ultimately you may be subject to the strict requirements anvi’o sets forth (for example, if a structure has a missing residue, you will hear about it). In particular, the amino acid sequence in each structure file must match the sequence anvi’o has for that gene (from the contigs-db, or from the genomes-storage-db for a pangenome).
Edit this file to update this information.