****************************************************
        *                ViewModel (v1.2)                  *
        * A package to build and visualize macromolecular  *
	*      surface with DiSCO charges in MATLAB        *
        *           Copyright (c) February 2001            *
        *               Update March 2001 by               *
        *   Qing Zhang, Daniel A. Beard, & Tamar Schlick   *
        *   Department of Chemistry, New York University   *
        ****************************************************

                           
0. REFERENCE
			   
   Zhang, Q., Beard, D. A., & Schlick, T., 
   Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DiSCO) algorithm. 
   J. Comput. Chem., 24: 2063-2074, 2003.

   [This paper presents Irregular DiSCO Model Building Procedure (Figure 3), which is also used in ViewModel to build the surface. Then the surface and surface charges are visualized by ViewModel in MATLAB.]
   
   

1. SYSTEM REQUIREMENTS

   MATLAB 5.3 or higher



2. INSTALLATION

   2.1. Unzip the downloaded package using tar or unzip. You will see a directory ViewModel-1.2 containing 5 files and one directory:
   
            NAME               TYPE                    FUNCTION
	README             ascii                   This manual.
        viewmodel.m        MATLAB M-function       Surface visualization routine (main program).
        dsurfa.c           C MEX-file              Surface building routine (source code).
        drawball.m         MATLAB M-function       Surface charge drawing routine (called by viewmodel).  
        Makefile           ascii                   Compiling dsurfa.c to dsurfa.* (makefile).
	example/           directory               Example (nucleosome core particle, used in the above paper)
  
   2.2. Check "Makefile" to see if there is any setting that should be changed according to your machine's environment and MATLAB location.
   
   2.3. Type:
            make
        A MATLAB MEX-function file starting with "dsurfa" will be produced. The extension of the filename depends on the system of your machine. For example, "mexsg64" on SGI/IRIX64, "dll" on Windows. The file has a DiSCO surface building routine called by viewmodel. 



3. RUN

   3.1. Start MATLAB (same version as described in "Makefile") in the ViewModel-1.2 directory.

   3.2. Type:
            help viewmodel
        You can see clearly how to use viewmodel() to visualize models.
	
        NOTE: The distance between the surface and the coordinate center of the macromolecule has been reduced by 2 Angstrom (by LOMINUS), which can make the surface charges more viewable. If you want to change this setting, please change LOMINUS value in the file "viewmodel.m".



4. CONTACT

Thank you for using ViewModel! If you have any question, bug finding, or good thought, please contact me in either of the following ways:

Email: qz219@nyu.edu
Phone: 212-998-3593


=======================================
Qing Zhang
Department of Chemistry 
New York University
31 Washington Place, Rm. 1021 Silver
New York, NY 10003
U.S.A.
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