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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
       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.