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NAME

       gamgi - general atomistic modelling graphic interface

SYNOPSIS

       gamgi [file_1.xml] ...  [file_n.xml]

DESCRIPTION

       gamgi is a computer package to construct, view and analyse atomic structures.

OPTIONS

       file_n.xml is a fullname such as:

	   ../dat/molecule/flavors/garlic.xml
	   ~/gamgi/dat/molecule/flavors/garlic.xml
	   http://www.gamgi.org/dat/molecule/flavors/garlic.xml
	   ftp://ftp.gamgi.org/gamgi/dat/molecule/flavors/garlic.xml

       Object  and config data can be mixed, so file_1.xml might be a preferences file, loaded before the other object files. To automate the pro-
       cedure, just add a line as this to ~/.bashrc:

	      alias gamgi='gamgi ~/gamgi/my_defaults.xml'

ENVIRONMENT

       GAMGI_HELP
	      Set this variable to let GAMGI know where the Help documentation files are.  For example, add a line as this to ~/.bashrc :

	      GAMGI_HELP=~/gamgi/gamgi/doc; export GAMGI_HELP

       GAMGI_TEXT
	      Set this variable to let GAMGI know where are the .ttf DejaVu files, to render solid fonts. For example,	add  a	line  as  this	to
	      ~/.bashrc:

	      GAMGI_TEXT=~/gamgi/gamgi/src/io/fonts; export GAMGI_TEXT

       BROWSER
	      Set this variable to let GAMGI know which browser to launch, in case this is chosen to read Help. For example, add a line as this to
	      ~/.bashrc:

	      BROWSER=firefox; export BROWSER

HELP

       Read introductory information with Help->Start. Browse the documentation at http://www.gamgi.org/ or its local copy at gamgi/doc/. Use  the
       help mechanisms reunited under the Help button. Subscribe the mailling list <gamgi-users@gamgi.org>.

       Contact the author at <jcgp07@gmail.com>.

       Throughout  all	interfaces  and  formats,  lengths are in angstrom, angles in degrees and decimal numbers are represented with dots. Every
       parameter that can be defined in an interface can be also defined in a file and vice-versa.

INTERFACES

       Rotate, move, scale the selected object pressing the left, middle, right mouse button. Export the selected  object  choosing  File->Export.
       The statusbar shows the selected object (left) and layer (right).

       To select an object, choose Object->Select and press over the object. Or choose the object class on the menu above, with the middle button,
       before pressing on the object. Or press twice Layer, Window or GAMGI on the menu above. When the object has no visual representation, press
       the mouse over the graphic area, to pop up a menu.

       To  select a layer, choose Layer->Select and press the mouse over the graphic area, to pop up a menu. Or choose the layer class on the menu
       above, with the middle button, before pressing the mouse over the graphic area, to pop up a menu.

       Solid objects usually require lights with diffuse and specular components to be properly represented in 3D space, otherwise they look flat.
       Wired objects do not have a 3D representation, so diffuse and specular lights are not reflected, becoming poorly visible when using lights,
       unless a significant ambient component is used. Often it is worth to draw solid and wired objects in different  layers,	with  and  without
       lights.

       When  a task dialog is open, to learn how it works, just select Help->Current and another dialog will pop up, explaining the meaning of all
       the parameters in the task dialog.

       To see detailed	explanations  of  GAMGI  interfaces,  consult  the  reference  manual  at  http://www.gamgi.org/interfaces/reference.html,
       doc/interfaces/reference.html or Help->Topic->Interfaces.

FORMATS

       GAMGI  can  import files in .xyz and .xml native format, selected automatically by the file extension. GAMGI can export files in .ps, .ppm,
       .jp[e]g, .png, .tif[f], .x3d and native .xml formats, selected automatically by the file extension.

       In GAMGI native XML format, a water molecule can be described as:

       <gml>
	 <molecule>
	   <atom element="O"  x="0.000" y="0.000" z="0.000" id="O1"/>
	   <atom element="H"  x="0.776" y="0.540" z="0.000" id="H1"/>
	   <atom element="H" x="-0.776" y="0.540" z="0.000" id="H2"/>

	   <bond parent1="O1" parent2="H1"/>
	   <bond parent1="O1" parent2="H2"/>
	 </molecule>
       </gml>

       To  see	detailed  explanations	of  GAMGI  formats,  consult  the   reference	manual	 at   http://www.gamgi.org/formats/reference.html,
       doc/formats/reference.html or Help->Topic->Formats.

EXAMPLES

       Choose Help->Tutorials to get a list of fully described procedures, exemplifying most aspects of the work with GAMGI.

SEE ALSO

       http://www.gamgi.org/

AUTHOR

       Written	by  Carlos Pereira <jcgp07@gmail.com>, helped by Steffen Moeller <moeller@debian.org> and Daniel Leidert <daniel.leidert@wgdd.de>,
       from the Debian project.

0.14.3								 November 30 2009							  GAMGI(1)