# Installing MCell (Linux and OSX)¶

Note

MCell is included in the CellBlender 1.1 bundle (linux, windows). You only need to install MCell separately if you would like to run it outside of CellBlender or if you are setting up CellBlender from scratch (as is needed on OSX).

## Extract MCell¶

The binary file that you download is a compressed file with a name that ends in ".zip". Open a terminal and navigate to where the file was downloaded (e.g. cd /home/user/Downloads). Alternatively, you can do this through a GUI file manager like Nautilus in Ubuntu, but we won't show that here.

Now, unzip the file by typing the following at the command line:

unzip mcell_3.4_linux.zip


If this succeeds, the file will no longer have the ".gz" suffix.

## Rename and Make Executable¶

Rename the file to something more convenient and make it executable, e.g.,

mv mcell_3.4_linux mcell
chmod a+x mcell


## Put MCell in a PATH Directory¶

Note

The .bash_profile is usually only updated when you login to the computer, so you may need to restart your computer or type source ~/.bash_profile.

## Test MCell¶

Verify that MCell is working by typing the following at the terminal:

mcell


If you have successfully put MCell in your PATH, you should see a startup message followed by an error that indicates no MDL (Model Description Language) file has been specified:

MCell: command-line argument syntax error: No MDL file name specified
MCell 3.4 (commit: 275420e  date: Thu, 29 Sep 2016 14:07:12 -0400)
Running on washburne at Fri Jan 27 11:14:11 2017

Copyright (C) 2006 - 2016 by
The National Center for Multiscale Modeling of Biological Systems,
The Salk Institute for Biological Studies, and
Pittsburgh Supercomputing Center, Carnegie Mellon University,

**********************************************************************
MCell development is supported by the NIGMS-funded (P41GM103712)
National Center for Multiscale Modeling of Biological Systems (MMBioS).
**********************************************************************

Usage: ./mcell_3.4_linux [options] mdl_file_name

options:
[-help]                  print this help message
[-version]               print the program version and exit
[-fullversion]           print the detailed program version report and exit
[-seed n]                choose random sequence number (default: 1)
[-iterations n]          override iterations in mdl_file_name
[-logfile log_file_name] send output log to file (default: stdout)
[-logfreq n]             output log frequency
[-errfile err_file_name] send errors log to file (default: stderr)
[-checkpoint_outfile checkpoint_file_name]  write checkpoint file
[-quiet]                 suppress all unrequested output except for errors
[-with_checks ('yes'/'no', default 'yes')]   performs check of the geometry for coincident walls