In this discussion, GEMSHOME is the location of your gems installation.
Finding the scripts
GEMS scripts exist in two places in the GEMSHOME directory tree:
- GEMSHOME/bin
- GEMSHOME/testbin.
The scripts in testbin are temporary and are generally used by developers to test their code. You are welcome to check them out, but since they might be temporary or change rapidly, we will make no attempt to formally document them. Note that some of them will only work, as-is, from within the testbin directory (meaning you might need write privileges there to use them).
However, the scripts in bin are considered to be somewhat stable. They have also been made to be somewhat user friendly and are documented. In general, they can be copied to a new location and used as-is or modified as needed. If you move or modify them, do be careful to update any dependencies. That is, if you change a script foo, that calls another script in GEMSHOME called bar, and you have also moved bar to a new location and/or changed it, don’t forget to update the relevant line in foo!
Prerequisites
Of course, GEMS scripts require that you have downloaded and compiled the gems/gmml combination. Please see the download and install instructions for more information.
Most GEMS scripts require that GEMSHOME be set, as an environment variable, to the location of your gems installation. For most Linux or Unix systems, one of the following will work:
For BASH-like shells:
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export GEMSHOME=/path/to/your/gems |
For CSH-like shells:
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setenv GEMSHOME /path/to/your/gems |
If your GEMSHOME is not set, the script will usually detect that and warn you about it.
Using the scripts
You will most likely want to add $GEMSHOME/bin to your path:
For BASH-like shells:
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export PATH=$GEMSHOME/bin:$PATH |
For CSH-like shells:
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setenv PATH $GEMSHOME/bin:$PATH |
After that, call the script according to the usage for the script. In general, you can get a usage statement by just entering the name of the command. For example:
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$ detect_sugars Usage: detect_sugars PDB_file.pdb The output goes to standard out (your terminal window, usually). So, alternately: detect_sugars PDB_file.pdb > output_file_name |
…then enter the command again with what the script requires, and go!
Script documentation
Click here to see a list of pages documenting usage of the scripts.