Applications Tutorial

You can use ProDy Applications to perform some automated tasks, such as ANM/GNM/PCA calculations, fetching and aligning PDB files, making atom selections, or identify contacts. ProDy applications are handled by a script that comes with all installation packages. You can run the script from a central location such as /usr/local/bin:

$ prody -h

or from the current working directory:

$ ./prody -h

or:

$ prody -h

or on Windows:

$ C:\Python27\Scripts\prody -h

These lines will print available ProDy applications. You can get more help on a specific commands as follows:

$ prody anm -h

Align PDB files

prody align command can be used to download and align structures for given PDB identifiers:

$ prody align 1p38 1r39 1zz2

Structures will be automatically downloaded from wwPDB FTP servers and saved in the current working directory. Additionally, you can configure ProDy to use a local mirror of PDB or to store downloaded files in a local folder. See ProDy Basics part of the tutorial.

ANM calculations

prody anm can be used to perform ANM calculations:

$ prody anm 1p38 -a -A

-a and -A options will make ProDy output all data and figure files.

PCA calculations

prody anm can be used to perform PCA calculations. The following example will perform PCA calculations for Cα atoms of the p38 MAP kinase using files:

$ tar -xzf p38_trajectory.tar.gz
$ prody pca -a -A --select calpha --pdb p38.pdb p38_100frames.dcd