pegi3s/ccp4 repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of CCP4⁠ (Collaborative Computational Project No. 4), a Software suite for Macromolecular X-Ray Crystallography, using command line operations.

⁠Note 1

This docker image runs version 7.0 of CCP4 and it assumes you accept the software license⁠ stated in /ccp4/conditions.txt.

This and other builds are available in this repository⁠.

⁠Using the CCP4 image in Linux

Although can be used for a variety of operations, here we demonstrate its use to run PISA⁠ (Proteins, Interfaces, Structures and Assemblies).

For this purpose, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/ccp4 bash -c "/ccp4/bin/run data/inputFolder data/outputFolder"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input folder with all protein structures you want to analyze. Additionally, this will be the same directory where a folder with the results will be created.
• /inputFolder to point to the folder that contains the protein structures to analyze.
• /outputFolder to point to the folder where sub-folders with the results for each submitted structure will be saved, as well as the configuration file for PISA.

⁠Note 2

You have the option to run the image without specifying the /inputFolder and the /outputFolder. If that is the case, this image will assume you have your input data in a folder named /input inside /your/data/dir and will save the results in a new folder, named /Results_CCP4-PISA. For this, adapt and run the command:

docker run --rm -v /your/data/dir:/data pegi3s/ccp4 bash -c "/ccp4/bin/run"

⁠Note 3

To see other options available with PISA inside CCP4, just run: pisa inside the docker image.

⁠Note 4

The values shown in the .tsv file generated when using the custom /ccp4/bin/run script are BSA values. The code (0 or 1) indicates whether the BSA value is 0 or above 0.