Microbial 'omics


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external-structures [artifact]

Table of Contents

TXT

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 or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

By default, anvi’o predicts protein structures using MODELLER when creating a structure-db. Yet, if the user provides an external structures file, then anvi’o does not perform template-based homology modelling, and instead uses this file to obtain the structure information for the structure-db.

External structures is a user-provided TAB-delimited file that should follow this format:

gene_callers_id path
1 path/to/gene1/structure.pdb
2 path/to/gene2/structure.pdb
3 path/to/gene3/structure.pdb
4 path/to/gene4/structure.pdb
7 path/to/gene5/structure.pdb
8 path/to/gene6/structure.pdb
(…) (…)

Each path should point to a protein-structure-txt.

Please note that anvi’o will try its best to test the integrity of each file, and work with any limitations, however ultimately the user may be subject to the strict requirements set forth by anvi’o. For example, if a structure has a missing residue, you will hear about it.

Edit this file to update this information.