Stc Example Summary
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basic:
    This example is John Bagu and Pierre Lavigne's data as
    described in the stc paper.

    1) Click on "calc ASA" button.
    2) Press "calculate" button.
        Done calculations, no errors.
    3) Click 'Display Results' and view accessible surface area file
        'out.complex.acc' file or other files, Click "Dismiss" when done.
    4) Click "Thermodynamics" button
    5) Press "Calculate". Click "Histograms" to see charts for the various
        thermodynamic variables for ligand/enzyme. Click "Dismiss" when you
        are done viewing results.
 
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batch_gui:
    This example shows how to use the batch button to process
    several pdb files (although only 3 in this case).
    
    When stc starts, press the "batch" button and then "calculate".
    All files with a '.pdb' suffix are processed, calculating ASA
    is done first and then thermodynamic calculations.
    
    Basic results are found in output_dir/*.basic.  Detailed results are found
    in output_dir/*.detail.  A summary of the results are in stc.batch.summary.
    Users can click on a particular results line to see thermodynamics results for
    that particular pdb.
 
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batch_script
    This example is on how to use a batch script to run stc without graphics.
    Users with many pdb inputs can have stc crank through all the results quickly.
    The script is in batch_stc and users should carefully study it.
    
 
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dimer:
    Unfolding example with residues unfolded specified in the defaults file 
    1) Click on "calc ASA" button.
    2) Press "calculate" button.
        Done calculations, no errors.
    3) Click "Thermodynamics" button, residues 64-69 are unfolded.
    4) Press "Calculate". Click "Dismiss" when you are done viewing results.
 
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dna: 
    This example uses nucleic acids and amino acids.
 
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err1: 
    This example demonstrates some common errors and how they were resolved.

    1) Click on "calc ASA" button.
    2) Press "calculate" button.
       Done calculations, display results, log file has some errors.
    3) Click 'Display results' and view log file to see these errors:

    *** Error, Unrecognized residue name:     850 CA   CA   160 ... 
    *** Error, Unrecognized atom name:     851 CA   CA   161    ...

    Let's say we choose to ignore these errors for now.
    4) Click "Dismiss".

    5) Click "Thermodynamics" button.
    6) Press "Calculate". This time thermo complains about the calcium atoms
    in the pdb file. Quit stc and go to pm.complex.pdb and remove the 
    offending atoms (bottom of the file). You can also comment them out by
    using the "#" function at the start of each line.
 
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jrb:
    This example is John Bagu and Pierre Lavigne's data as
    described in the stc paper.
 
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olig:
    Test for oligormization.
 
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plotsave:
    This example is the "basic" example testing plot saving. 
    Click "File->Save Window" and save any open stc window. 
    Click "File->Save Plot" and save stc histogram plots.
 
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pm1: 
    Pascal Mercier STC run
    This example demonstrates the use of a custom built sconf file for the enzyme

    Press both "calculate from datafile" radio buttons.
    This allows us to use the values found in the file pm.enzyme.sconf.
 
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xuw:
    Xu Wang STC run
    This example demonstrates the use of a custom built amino.def file for
    the EMD residue.

    1) Note that I have used the "stc.defaults" file to set the "Residue Library" to
     "custom.amino.def".  Look at this file to see how we added the EMD entity. 
    2) Click on "calc ASA" button.
    3) Press "calculate" button.
        Done calculations, no errors. 
    4) Click "Dismiss" if you are interested in viewing these intermediate files.
    5) Click "Thermodynamics" button.
    6) Press "Calculate". Click "Dismiss" when you are done viewing results.
 
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