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 5uoj 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 5uoj -a -A
-a and -A options will make ProDy output all data and figure files.