Download the file all.zip and unzip it. There are three platform-specific Makefiles:
Copy the file Makefile.[Your Platform] to a new file Makefile. For example, if you are using an Apple, copy Makefile.MacOSX to Makefile. Or, if you are using a Windows PC, install Cygwin (with at least these additional packages), then copy Makefile.Cygwin to Makefile.
To verify that everything works correctly, run the following four commands:
The first command make all compiles the programs.
The second command make PKB00001.result predicts the secondary structure of the sequence PKB00001 from PseudoBase. This command takes a few minutes to complete and generates three files:
The third command make PKB00001.show displays the predicted structure of PKB00001 using the visualization program. Press the escape key to exit from the visualization program.
The fourth command make PKB00001.movie shows a movie of the folding simulation of PKB00001 in real time. Press the escape key to exit from the visualization program.
The console output of the four commands should be similar to the following two screenshots:
