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<!DOCTYPE book PUBLIC "-//OASIS/DTD DocBookXML V4.1.2//EN"
"http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd"[
  <!ENTITY legal SYSTEM "legal.xml">
  <!ENTITY appversion "0.8.0">
  <!ENTITY manrevision "0.8.0">
  <!ENTITY date "Febrary 2006">
  <!ENTITY app "GChem3d Viewer">
]>
<!-- 
      (Do not remove this comment block.)
  Maintained by the GNOME Documentation Project
  http://developer.GNOME.org/projects/gdp
  Template version: 2.0 beta
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-->
<!-- =============Document Header ============================= -->
<book id="index" lang="en">
  <title>&app; manual</title>
<!-- please do not change the id; for translations, change lang to -->
<!-- appropriate code -->
  <bookinfo> 
	 <title>&app; Manual V&manrevision;</title>
	 <copyright> 
       <year>2006</year>
       <holder>Jean Bréfort</holder>
     </copyright>

  <!-- translators: uncomment this and add lang=".." to the <book> tag:

  <copyright>
   <year>2002</year>
   <holder>ME-THE-TRANSLATOR (Latin translation)</holder>
  </copyright>

   -->

	&legal;

	<publisher role="maintainer">
		<publishername>GNOME Documentation Project</publishername>
	</publisher>

	 <authorgroup> 
		<author> 
		  <firstname>Jean</firstname>
		  <surname>Bréfort</surname>
		  <affiliation> 
			 <address> <email>jean.brefort@normalesup.org</email> </address>
		  </affiliation>
		</author> 
<!-- This is appropriate place for other contributors: translators,
      maintainers,  etc. Commented out by default.
       <othercredit role="translator">
	<firstname>Latin</firstname> 
	<surname>Translator 1</surname> 
	<affiliation> 
	  <orgname>Latin Translation Team</orgname> 
	  <address> <email>translator@gnome.org</email> </address> 
	</affiliation>
	<contrib>Latin translation</contrib>
      </othercredit>
-->
	 </authorgroup>

<!-- According to GNU FDL, revision history is mandatory if you are -->
<!-- modifying/reusing someone else's document.  If not, you can omit it. -->
	 <revhistory>
<!-- Remember to remove the &manrevision; entity from the revision entries other
   than the current revision. -->
   		<revision> 
		  <revnumber>&app; Manual V&manrevision;</revnumber>
		  <date>&date;</date> 
		  <revdescription> 
			 <para role="author">Jean Bréfort
				<email>jean.brefort@normalesup.org</email> </para>
			 <para role="publisher">GNOME Documentation Project</para>
		  </revdescription>
		</revision>
	 </revhistory>
	 <releaseinfo> This manual describes version &appversion; of &app;.
		</releaseinfo>
	 <legalnotice> 
		<title>Feedback</title>
		<para>To report a bug or make a suggestion regarding the &app; application or
		this manual, go to the
		<ulink url="http://savannah.nongnu.org/projects/gchemutils" type="html"><application>&app;</application> home page</ulink>. 
      </para>
<!-- Translators may also add here feedback address for translations -->
	 </legalnotice>
	<abstract role="description">
		<para>&app; allows you to display molecular structures.</para>
	</abstract>
  </bookinfo>  

<!-- ============= Document Body ============================= -->

<!-- ============= Introduction ============================= -->
 <preface id="gchem3d-viewer-intro">
    <title>Introduction</title>
	<para>The <application>&app;</application> application is a simple
	molecular structures visualizer.</para>

 </preface>

<!-- ============= Getting started ============================= -->
 <chapter id="gchem3d-viewer-getting-started">
    <title>Getting started</title>
	<sect1 id="gchem3d-viewer-to-start">
		<title>To Start &app;</title>
		<para>You can start <application>&app;</application> in the following ways:</para>
		<variablelist>
    		<varlistentry>
    		<term><guimenu>Applications</guimenu> menu</term>
    		<listitem>
    		<para>Choose 
    		<menuchoice>
    		<guisubmenu>Education</guisubmenu>
    		<guimenuitem>Molecules Viewer</guimenuitem>
    		</menuchoice>. </para>
    		</listitem>
    		</varlistentry>
    		<varlistentry>
    		<term>Command line</term>
    		<listitem>
    		<para>Type <command>gchem3d-viewer</command>, then press <keycap>Return</keycap>.</para>
    		</listitem>
    		</varlistentry>
    		</variablelist>
	</sect1>
	<sect1 id="gchem3d-viewer-when-you-start">
		<title>When You Start &app;</title>
		<para>When you start <application>&app;</application>, the following window is displayed:</para>
 			<figure id="gchem3d-viewer-main-window"> 
			  <title>&app; main window</title>
			  <screenshot> 
					<mediaobject>
						<imageobject>
							<objectinfo> <abstract><para>Screenshot of the <application>&app;</application> main window.</para></abstract>
							</objectinfo> 
							<imagedata fileref="figures/main-window.png"/>
						</imageobject>
					</mediaobject>
				</screenshot>
			</figure>
	
		<para>The <application>&app;</application> window contains the following
		  elements: </para>
		<variablelist> 
		  <varlistentry> <term>Menubar</term> 
			 <listitem> 
				<para>The menus on the menubar contain all of the commands you need
				  to work with files in <application>&app;</application>.</para>
			 </listitem>
		  </varlistentry>
		  <varlistentry> <term>Display area</term> 
			 <listitem> 
				<para> The display area contains the contents of an opened file
				if any. </para>
			 </listitem>
		  </varlistentry>
		</variablelist>
	</sect1>
	<sect1 id="gchem3d-viewer-open-file">
		<title>To Open a File</title>
		<para>To open a file, choose 
		  <menuchoice> <guimenu>File</guimenu> <guimenuitem>Open</guimenuitem>
			 </menuchoice>
		  to display the <guilabel>Open File</guilabel> dialog. Select the file
		  that you want to open, then click <guibutton>OK</guibutton>. The file is
		  displayed in the <application>&app;</application> main window. </para>
		<para><application>&app;</application> can open files on a distant server using the Gnome Virtual
		File System.</para>
		<para><application>&app;</application> can open several file formats. Available formats are:</para>
		<itemizedlist> 
		  <listitem><para>ChemML files (*.cml)</para>
		  </listitem>
		  <listitem><para>MDL MOL files, MDL Structure Data files (*.mol;*.sd;*.sdf)</para>
		  </listitem>
		  <listitem><para>PDB files (*.pdb;*.ent)</para>
		  </listitem>
		  <listitem><para>XYZ Coordinate Format files (*.xyz)</para>
		  </listitem>
	  </itemizedlist>
	  <para>You can open multiple files in <application>&app;</application>.
	  The application displays each file in its own window.</para>
	  <para>Recently opened file appear in the <menuchoice> <guimenu>File</guimenu>
	   <guimenu>Open recent</guimenu></menuchoice> sub-menu.</para>
	</sect1>
	<sect1 id="gchem3d-viewer-run-from-cmd-line">
		<title>To Open Multiple Files from a Command Line</title>
		<para>You can run <application>&app;</application> from a command line
		  and open a single file or multiple files. To open multiple files from a command
		  line, type the following command, then press <keycap>Return</keycap>:</para>
		<para><command>gchem3d-viewer <replaceable>file1 file2 file3</replaceable></command></para>
	</sect1>
</chapter>

<chapter id="gchem3d-viewer-usage">
    <title>Usage</title>
	<sect1 id="gchem3d-viewer-save-as-image">
		<title>To Save the View as an Image</title>
		  <para>To open a file, choose 
		  <menuchoice> <guimenu>File</guimenu> <guimenuitem>Save as Image...</guimenuitem>
			 </menuchoice>
		  to display the <guilabel>Save as image</guilabel> dialog. Select a
		  file name and, if wanted, a file type, then click
		  <guibutton>OK</guibutton>.</para>
		  <para>Supported types are VRML, and all types that GdkPixbuf can export.
		  You'll find an exact list in the drop-down file type menu.</para>
		  <para>If no file type is specified, <application>&app;</application>
		  tries to determine the type from the file name. If it does not succeed,
		  the default type (VRML) will be used.</para>
		  <para>An appropriate extension will be added to the file name if none
		  is found.</para>
		  <para>PostScript and PDF files can also be obtained with the <link
 		  linkend="gchem3d-viewer-print">Print command</link>.</para>
	</sect1>
	<sect1 id="gchem3d-viewer-print">
		<title>To Print the View</title>
		  <para>To open a file, choose 
		  <menuchoice> <guimenu>File</guimenu> <guimenuitem>Print...</guimenuitem>
			 </menuchoice>.</para>
		<para><application>&app;</application> uses a 300 dpi resolution
		when printing.</para>
		<para>You might want to <link linkend="gchem3d-viewer-background">
		change the Background color</link> before printing.</para>
	</sect1>
	<sect1 id="gchem3d-viewer-mode">
		<title>To Change the Model Options</title>
		<para><application>&app;</application> id able to display a molecule
		using two model types: the ball ans stick model and the compact
		model. The first one is the default.</para>
		<para>To change the mode, choose either <menuchoice> <guimenu>View</guimenu> <guimenuitem>Balls and sticks</guimenuitem>
			 </menuchoice> or <menuchoice> <guimenu>View</guimenu><guimenuitem>Space filling</guimenuitem>
			 </menuchoice>.</para>
		<para>You can also change the orientation. Just click somewhere in
		the view and drag the mouse until you get the wanted orientation.</para>
	</sect1>
	<sect1 id="gchem3d-viewer-background">
		<title>To Change the Background Color</title>
		<para>To change the backgound color, choose 
		  <menuchoice> <guimenu>View</guimenu> <guimenuitem>Background color</guimenuitem>
			 </menuchoice> and select the appropriate color in the palette, or
			 choose a custom color.</para>
	</sect1>
	<sect1 id="gchem3d-viewer-question">
		<title>To Ask a Question</title>
		<para>If you choose <menuchoice> <guimenu>Help</guimenu> <guimenuitem>Ask a question</guimenuitem></menuchoice>,
		your mail agent should pop up with a new message to the <ulink type="mail" url="mailto:gchemutils-main@nongnu.org">Gnome Chemistry Utils
		mailing list</ulink>.</para>
		<para>Another way to get some help is to connect on the #gchemutils channel
		at irc.gimp.net and ask your question there (if you are not alone on the channel).</para>
	</sect1>
	<sect1 id="gchem3d-viewer-web">
		<title>To Find the Gnome Chemistry Utils on the Web.</title>
		<para>If you choose <menuchoice> <guimenu>Help</guimenu> <guimenuitem>Gnome Chemistry Utils on the web</guimenuitem></menuchoice>,
		the default web browser should pop up and display the main page for the Gnome Chemsitry Utils.</para>
		<para>The main page is
		<ulink type="http" url="http://gchemutils.nongnu.org">http://gchemutils.nongnu.org</ulink> and the project
		page at savannah <ulink type="http" url="http://savannah.nongnu.org/projects/gchemutils">http://savannah.nongnu.org/projects/gchemutils</ulink>.</para>
	</sect1>
	<sect1 id="gchem3d-viewer-bug">
		<title>To Report a Bug</title>
		<para>To report a bug, you must use the bug page for the Gnome Chemistry
		Utils at Savannah. You can access it by choosing
		<menuchoice> <guimenu>Help</guimenu> <guimenuitem>Report Bugs</guimenuitem></menuchoice>
		(hopefully you'll have only one at once to report).</para>
		<para>You can also type the bug report page address directly in
		the browser. The bug repository is at
		<ulink type="http" url="https://savannah.nongnu.org/bugs/?group=gchemutils">https://savannah.nongnu.org/bugs/?group=gchemutils</ulink></para>
	</sect1>
</chapter>

 <!-- ============= Application License ============================= -->

 <chapter id="license">
  <title>License</title>
  <para>
   This program is free software; you can redistribute it and/or
   modify it under the terms of the  <ulink type="help" url="ghelp:gpl">GNU
   General Public License</ulink> as
   published by the Free Software Foundation; 
   either version 2 of the License, or (at your option) any later
   version.
  </para>
  <para>
   This program is distributed in the hope that it will be useful, but
   WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   <citetitle>GNU General Public License</citetitle> for more details.
  </para>
  <para>
   A copy of the <citetitle>GNU General Public License</citetitle> is
   included as an appendix to the <citetitle>GNOME Users
   Guide</citetitle>.  You may also obtain a copy of the
   <citetitle>GNU General Public License</citetitle> from the Free
   Software Foundation by visiting <ulink type="http"
   url="http://www.fsf.org">their Web site</ulink> or by writing to
   <address>
    Free Software Foundation, Inc.
    <street>51 Franklin St</street> - Fifth Floor
    <city>Boston</city>, <state>MA</state> <postcode>02111-1307</postcode>
    <country>USA</country>
   </address>
  </para>
 </chapter>

</book>
