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 procedure, 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.