Sophie: kmovisto-0.7.0-1mdk i586

kmovisto-0.7.0-1mdk.i586.rpm

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<H2><A NAME="s3">3. General Usage </A></H2>
<P>
<H2><A NAME="ss3.1">3.1 Run KMovisto</A>
</H2>
Start the program by typing kmovisto (or /usr/bin/kmovisto if the directory
/usr/bin is not part of the search path). If you start kmovisto
the first time, the file .kmovisto will be created in your home directory specified
by the environment variable HOME. This file is for storing parameters for your
individual program settings.
<P>
<H2><A NAME="ss3.2">3.2 Import Files</A>
</H2>
The first step in using KMovisto is to import an input file. As described in the introduction,
you are able to load  GAUSSIAN 94 or GAUSSIAN 98 files or <A HREF="index-4.html">XYZ files</A>.
There are two ways to do this: Use the <I>File->Import</I> menu and select the file or - the
easiest way - press the corresponding import button (yellow arrows down) from the toolbar
(<B>Fig. 2</B>).
<P>
<DIV align="center"><img src="./images/toolbar.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 2:</B> Toolbar of KMovisto
</PRE>
</BLOCKQUOTE></CODE>
<P>
<B>Fig. 3</B> shows the result of importing the <A HREF="index-4.html">XYZ file</A> of MeS(S)OMe.
<P>
<DIV align="center"><img src="./images/kmovisto.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 3:</B> KMovisto after importing a file
</PRE>
</BLOCKQUOTE></CODE>
<P>
Press the left mouse button and move the mouse up and down or left and right to rotate the molecule
arround the x axis respectively the y axis. If you hold down the CTRL key during this procedure,
the molecule rotate arround the z axis which points in your direction.
Translations are performed by mouse movements while pressing the SHIFT key and left mouse button.
Press the middle mouse button to reset the translations or rotations you made.
You can also zoom the molecule if you press only the right mouse button and move up
or down.
<P>
<H2><A NAME="ss3.3">3.3 Molecule Changings</A>
</H2>
All changes at the molecule are made in the <I>Molecule</I> menu. Select the <I>Atoms</I> submenu for
changing atom properties. The following dialog box appears (<B>Fig. 4</B>):
<P>
<DIV align="center"><img src="./images/dialog_atoms.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 4:</B> Dialog box for changing atom parameters
</PRE>
</BLOCKQUOTE></CODE>
<P>
Chose the atom you search for in the listbox and change it's color, radius or OpenGL structure. Larger
radii maybe result in drawing new bonds where you don't expect them.
If there are bonds connecting the 'wrong' atoms you simply switch to edit mode. See <A HREF="index-4.html#ss4.5">chapter 4.5</A>
for further informations.
<P>
To change the bond properties you should select the <I>Bonds</I> submenu.
(<B>Fig. 5</B>).
<P>
<DIV align="center"><img src="./images/dialog_bonds.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 5:</B> Dialog box for changing bond parameters
</PRE>
</BLOCKQUOTE></CODE>
<P>
The bond fudge parameter detemines the bond tendency in general: Bonds are drawn between
atoms with large radii and if the bond fudge parameter is set to a large value. In some cases,
there are bonds drawn between atoms, which are not connected if you consider the 'chemical
intuition' so you can delete or define new bonds as described in <A HREF="index-4.html#ss4.5">chapter 4.5</A>.
Of course, you also can change the bond color,
which is used for displaying the molecule. How to change the bond color used for exporting
POV-Ray or VRML files see <A HREF="index-3.html#ss3.4">chapter 3.4</A>.
<P>The next submenu called <I>Molecule->Appearance</I> is usefull to to adapt the look of the molecule
in KMovisto (<B>Fig. 6</B>).
<P>
<DIV align="center"><img src="./images/dialog_appearance.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 6:</B> Dialog box for changing the appearance of the molecule
</PRE>
</BLOCKQUOTE></CODE>
<P>
This dialog allows to change the atom size or the perspective of the molecular model.
A useful option is the ability to set labels on all atoms of the molecule. You can select
three types of labeling or disable it. In tabsheet <I>Background Color</I> you have the
ability to change the background color for OpenGL, flat mode and printings. Anaglyphic modes
allows only black or white background colors so the background color is calculated from
the sum of red, green and blue component of a given color.
<P>
At least, you maybe want to change the document title. Use the <I>Molecule->Title</I> submenu (<B>Fig. 7</B>)
for this purpose.
<P>
<DIV align="center"><img src="./images/dialog_title.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 7:</B> Dialog box for changing the title of the molecule
</PRE>
</BLOCKQUOTE></CODE>
<P>
<H2><A NAME="ss3.4">3.4 Export Files</A>
</H2>
Now you are able to export the molecule data. To do this use the <I>File->Export</I> submenu, select an
export format or press the corresponding export button (yellow arrows up) from the toolbar (POV-Ray, VRML
or <A HREF="index-4.html">XYZ format</A>) and define a filename (see <B>Fig. 2</B> in chapter
<A HREF="index-3.html#ss3.2">3.2</A>.
<P>
To define your individual POV-Ray settings choose <I>POV-Ray</I> from the <I>Preferences</I> menu. Select
one of the tab sheets to change parameters. The <I>Atoms</I> (<B>Fig. 8</B>) sheet allows to set parameters
for drawing atoms as texture, atom color and atom size.
<P>
<DIV align="center"><img src="./images/dialog_povray_tab1.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 8:</B> Dialog box for changing POV-Ray atom parameters
</PRE>
</BLOCKQUOTE></CODE>
<P>
The second tab sheet (<B>Fig. 9</B>) is for setting up the bond parameters for the POV-Ray export file. You
are able to set the bond color and the bond radius.
<P>
<DIV align="center"><img src="./images/dialog_povray_tab2.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 9:</B> Dialog box for changing POV-Ray bond parameters
</PRE>
</BLOCKQUOTE></CODE>
<P>
While the first two tab sheets allow to change the molecule rendering properties the last two tab sheets are
for light and camera setting purposes. As <B>Fig. 10</B> shows the third tab sheet makes it possible for you
to define up to three light sources and enable or disable the <I>Shadowless</I> option.
<P>
<DIV align="center"><img src="./images/dialog_povray_tab3.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 10:</B> Dialog box for changing POV-Ray light parameters
</PRE>
</BLOCKQUOTE></CODE>
<P>
To adjust the camera position and settings use the last tab sheet named <I>camera</I> (<B>Fig. 11</B>). <I>Right</I>
and <I>Up</I> means the width to heigth ratio. This depends on the current display resolution you use. For
a resolution of 640 to 480 pixels for example take the default value of -1.33333 for the x axis. <I>Direction</I>
means the direction of the camera. It is recommended to use the same view direction as KMovisto does, so take
the default value. The <I>Location</I> vector is suitable to adjust the distance between camera and molecule.
This value depends on the molecule size. Start with six or seven for small molecules and test the results. At least
the <I>Look At</I> vector defines the origin.
<P>
<DIV align="center"><img src="./images/dialog_povray_tab4.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 11:</B> Dialog box for changing POV-Ray camera parameters
</PRE>
</BLOCKQUOTE></CODE>
<P>
With KMovisto you are able to export VRML files too. To define your individual VRML settings choose <I>VRML</I> from
the <I>Preferences</I> menu. The first tab sheet named <I>Atoms</I> (<B>Fig. 12</B>) is for setting an alternate atom
color and atom radius.
<P>
<DIV align="center"><img src="./images/dialog_vrml_tab1.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 12:</B> Dialog box for changing VRML atom parameters
</PRE>
</BLOCKQUOTE></CODE>
<P>
You also want to change the bond parameters in your VRML sceene. To do this use the following tab sheet
named <I>Bonds</I> (<B>Fig. 13</B>). In this tab sheet you are able to change the bond radii and define
an alternate bond color.
<P>
<DIV align="center"><img src="./images/dialog_vrml_tab2.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 13:</B> Dialog box for changing VRML bond parameters
</PRE>
</BLOCKQUOTE></CODE>
<P>
The third and last tab sheet of the <I>Appearance->VRML</I> dialog named <I>Appearance</I> (<B>Fig. 14</B>) is
for setting up VRML specific properties such as texture and meterial node parameters. If you enable texture mapping
you are able to define an image file (JPEG, PNG or GIF format) which is mapped on your molecule. The material
section is to define color settings and define the shininess. The color is calculated by KMovisto as follows: The
red green blue values of each atom are multiplied by a factor between 0 and 1 depending on the slider position.
<P>
<DIV align="center"><img src="./images/dialog_vrml_tab3.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 14:</B> Dialog box for changing VRML appearance parameters
</PRE>
</BLOCKQUOTE></CODE>
<P>
To simplify the work with KMovisto, the dialog <I>Directories</I> (<B>Fig. 15</B>) found at <I>Preferences->Directories</I>
allows you to define working directories and file format filters. You are also able to define working directries
for use with file import or export plugins if supported. For further informations about plugins see <A HREF="index-6.html">chapter 6</A>.
<P>
<DIV align="center"><img src="./images/dialog_directories.jpg"></DIV>
<P>
<BLOCKQUOTE><CODE>
<PRE>
<B>Fig. 15:</B> Dialog box for changing working directories
</PRE>
</BLOCKQUOTE></CODE>
<P>
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