VMD 1.6 and later contain an embedded, fully-functional Python interpreter. The interpreter acts just like the Python command line: you can import your own modules and run them from with the text console of VMD. In addition, VMD provides a number of modules for loading molecules and controlling their display.
Pre-compiled VMD binaries currently use Python version 2.5. The current VMD source code has been tested to compile with Python versions 2.4 to 2.6 on a few platforms. User contributed VMD rpm or deb packages can be thus be compiled against any of those versions.