Brian Sykes Lab

Version: 6.0.4 - Feb / 2012
Download and Installation

Purpose: Stc - Structural Thermodynamics Calculations
A program which performs free energy calculations from the structure of different complexes.

Table of Contents

  1. Introduction

  2. Using the Software


References, Acknowledgements, and Copyright

Download and Installation

  1. This software is a self contained tcl/tk starkit which should make installation fairly trivial. See the Release notes for the latest updates. Download the software appropriate for your machine:

  2. Macosx - Double click the download file. You should now get a new file on the desktop (or your download directory) represented by the stc icon. You should be able to double click the icon to run the program.

    Linux - Same as the macosx procedure but you may have to drag the directory from the opened window to the desktop. If this is not working then use a terminal command like:

    	tar xvf stc*.tar
    to get the stc directory and then move it to the desktop.

  3. Next, let's make sure the software is working and we understand the data files required. Download data and examples (11MB) and follow the procedure above to create the stc-6.0-x-examples folder. (see the examples.readme file for a quick summary of each example provided).

  4. To run an example, double click on the stc.command file packaged within each example directory. For linux, you may get a dialog asking what to do next, just click on the "Run" button.

  5. Finally, if you wish to keep the software in a more permanent location, pick one of the methods below:

Setup your Data

  1. Create a working directory.
  2. Copy structure files here (pdb format).

  3. (optional) Create an stc.defaults file to customize how this software runs.
  4. (optional) Copy a custom residue library here.
  5. (optional) Copy each custom ASA file here.
  6. (optional) Copy each custom sconf file here.
The data and examples file contain many examples demonstrating the input above.

The Initial STC window

The Calc ASA window

The Thermodynamics Window

Output - Basic results

Output - Verbose results

Output - histograms

Multiple Structures

Multiple Structure Scripts


Back to stc home

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