Environment Variable MOL_PATH

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The environment varible MOL_PATH may be used to define the list of directories which should be searched when you are trying to load certain PDB file. It is not mandatory to define this environment variable, but it is very practical.

MOL_PATH is not the only environment variable recognized by garlic. There is also MOL_DIR, but it is capable to specify only one directory, so it is not recommended.

The exact procedure which should be used to define the environment variable MOL_PATH depends on the shell you use. The procedure is described here for some commonly used shells.

If you don't know what is you shell, execute these commands:

echo $shell
echo $SHELL

Bourne Shell

If you are using the Bourne shell (sh) or the GNU clone called Bourne-again shell (bash), use the example bellow to create your own MOL_PATH variable. Use colon ( : ) to separate directories. It is important to export the variable! You should define this variable through your .bash_profile or .bashrc resource file in your home directory. Don't forget to replace the user name and directories.

MOL_PATH="/home/zucic/pdb:/home/zucic/glob:/home/zucic/memb"
export MOL_PATH

C Shell

If you are using the C shell (csh) or it's clone tcsh, use the command setenv to define the environment variable MOL_PATH. Use colon ( : ) to separate directories. You should define this variable through your .cshrc, .tcshrc or .login resource file in your home directory. The user name and directories should be replaced, of course.

setenv MOL_PATH /home/zucic/pdb:/home/zucic/glob:/home/zucic/memb

Other Shells

For other shells, read the manual page to learn how to define the environment variable MOL_PATH. In most cases, the method is similar to one of the methods described above.