anvi-setup-pdb-database

Setup or update an offline database of representative PDB structures clustered at 95%.

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Authors

Evan Kiefl
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Requires

This program seems to know what its doing. It needs no input material from its user. Good program.

Provides

pdb-db

Usage

Basic usage

This program creates a pdb-db local database that holds PDB structures from this sequence database, which is hosted by the Sali lab. Their database comprises all PDB RCSB sequences that have been clustered at 95% sequence similarity. They seem to update their database every couple of months (thank you guys!).

The purpose of anvi-setup-pdb-database to have a local copy of reference structures that can be used to, for example, get template structures for homology modelling when anvi-gen-structure-database is ran.

Running this program is easy:

anvi-setup-pdb-database --just-do-it

If you already have a pdb-db artifact and are trying to redownload this data, run

anvi-setup-pdb-database --reset

Or if you just want to update your database, run

anvi-setup-pdb-database --update

Notes

The output pdb-db database is ~20GB and its contents may take several hours to download.

Edit this file to update this information.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-setup-pdb-database.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-setup-pdb-database [-h] [--pdb-database-path PATH] [-T NUM_THREADS] [--update] [--skip-modeller-update] [--reset]

Parameters and their descriptions

options
--pdb-database-path PATH
The path for the PDB database to be stored. If you leave it as is without specifying anything, anvi'o will set up everything in a pre-defined default directory. The advantage of using the default directory at the time of set up is that every user of anvi'o on a computer system will be using a single data directory, but then you may need to run the setup program with superuser privileges. If you don't have superuser privileges, then you can use this parameter to tell anvi'o the location you wish to use to setup your database.
-T, --num-threads NUM_THREADS
Maximum number of threads to use for multithreading whenever possible. Very conservatively, the default is 1, unless the environmental variable `ANVIO_THREADS` sets another positive integer. If you use this parameter, it will override `ANVIO_THREADS`. It is a good idea to not exceed the number of CPUs / cores on your system. Plus, please be careful with this option if you are running your commands on a SGE -- if you are clusterizing your runs, and asking for multiple threads to use, you may deplete your resources very fast. Default: 1
--update
Use this flag if you would like to update your current database.
--skip-modeller-update
By default, MODELLER's search DB is updated when this program is ran so that if MODELLER finds a protein, its structure is guaranteed to be in this database. If you don't want to touch the MODELLER database, use this flag.
--reset
Remove all the previously stored files and start over. If something is feels wrong for some reason and if you believe re-downloading files and setting them up could address the issue, this is the flag that will tell anvi'o to act like a real computer scientist challenged with a computational problem.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.

Copyleft, The anvi'o Project