Where should be muscle or dssp placed ?

[Former user]

What is the suggested location of muscle or dssp that is required by various bio3d functions? Since not all functions have exefile option is it mandatory to change the function or there is a way to set a path to the executables within R environment? Thank you.

[Xinqiu Yao]

Hi,

We expect all functions calling dssp and/or muscle should have "exefile" option or the "..." that passed to functions having it. Just let us know if you find any function missing it. Ideally, the programs should be in the "search path" of your local system. For example, if you are using linux, you can add the program path to the configuration file .bashrc under your home directory:

export PATH=$PATH:/path/to/your/program

For Windows, right click "My computer" -> click "Change settings" -> Advanced -> Environment Variables -> From "System variables" list find "Path" and click "Edit" -> Add the path to your programs at the end of the line. This works for windows7 and may vary a little bit for other windows versions.

To test if above setting works, open a command line terminal (For windows, start->in the bottom box type "cmd" and return) and type dssp/muscle and return. It should give you the help message of the program.

Let me know if you still have problems.

[Barry Grant]

Good explanation Xinqiu. I will just add that if you are on Mac OS X then things are quite similar to the linux instructions that you listed.

For example you can find out whats in your path by launching Terminal in Applications/Utilities and entering:

echo $PATH

And the result should be like this…

/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin

So this is stating that you can run Unix style applications located in 5 default locations of path in the filing system:

/usr/bin
/bin
/usr/sbin
/sbin
/usr/local/bin

You can add extra locations to your path by creating or editing an existing .bash_profile file in your home directory. This file should contain a line like the following:

export PATH="/my/new/path:$PATH"  

You can now put muscle and dssp in any of the locations listed by echo $PATH, including /my/new/path/, which of course you should change to something sensible for you.

[Xinqiu Yao]

Thanks Barry! I missed MacOSX.

[Barry Grant]

I am marking this as resolved but will note that some of the explanation above could be added to the installation instructions on the main website.

Also the main websites installation instructions page ( http://thegrantlab.org/bio3d/tutorials/installing-bio3d ) could in general be simplified and better organized - I will add this to the ToDo list.