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.