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LineShapeKin Simulation

Getting started





Using the online version (web-interface)

We created a web-interface for LineShapeKin Simulation located at Kovrigin Lab server (Marquette University). This is "the first approximation" to a fully functional interface; therefore, your best option is still installing the code locally as described in the next sections.

I apologize, the online LineShapeKin Simulation is unaccessible due to the server malfunction.





Installation of the common files and setting the environment

This step is required whether you intend to use M-code or binaries.

Download and unpack the in the convenient location.

File index.htm is the main LineShapeKin Manual. However, you should use online manuals if possible because they are likely most up-to-date.

Please, make sure you are using C-shell or TC-shell as the terminal shell interpreter.

The LineShapeKin calls the Python programs to prepare input and output for the simulations from the folder LineShapeKin_Simulation_4.1/Python/. Add a path to this folder in your ~/.cshrc (OS X, Linux):

set path = ($path path-to-this-Python-folder-on-your-computer )


See a known problem with MATLAB using wrong shell interpreter




Using the M-code

  1. Set paths:
    In MATLAB set File:Set Path to the folder Matlab_code/ with an option "Unclude subfolders" or set additional path to Matlab_code/Models/.

2.  Test operation of the program:
     On a MATLAB command line type Simulate. You should see the following output:

>> Simulate

LineShapeKin Simulation ver. 4.1.1 6/12/09.
Evgenii Kovrigin, Medical College of Wisconsin

Usage: Simulate general_setup_name model_setup_name


3. Set up a simulation run:
Create a folder for you simulation anywhere. Change your MATLAB working directory to this location. Proceed with setting up your model as described in the Tutorial section Basic features of the package and an example of the simple binding process, no coupled equilibria. U model.


The known problem observed on OS X Mountain Lion: MATLAB calling the wrong shell interpreter for system commands

MATLAB may be using BASH for executing system commands (my python programs) instead of C-shell or TC-shell. You can check whether your MATLAB is using BASH by issuing the following command on the command line:

>> system('tell-me-shell-name')

The BASH output will be:

/bin/bash: tell-me-shell-name: command not found

If you have C-shell, the output does not mention BASH:

tell-me-shell-name: Command not found.

If you see your MATLAB uses BASH you need to include two lines in the .cshrc:

setenv MATLAB_SHELL /bin/tcsh
alias matlab 'open /Applications/'

The second line should include path to your MATLAB installation with the correct name (I show here path and package name as it is on my computer).

After these lines were included, type in the Terminal prompt:

source ~/.cshrc

When MATLAB opens, try 'system('tell-me-shell-name')' again.

NOTE: If you had to use this modification (your MATLAB uses BASH by default), you will have to always launch MATLAB from the command line for LineShapKin Simulation because the above modification to .cshrc is ignored if MATLAB is started from Dock.




Using the binaries