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## 3. General Usage

## 3.1 Run KMovisto

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.

## 3.2 Import Files

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 XYZ files. There are two ways to do this: Use the File->Import menu and select the file or - the easiest way - press the corresponding import button (yellow arrows down) from the toolbar (Fig. 2).

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>     Fig. 2: Toolbar of KMovisto

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Fig. 3 shows the result of importing the XYZ file of MeS(S)OMe.

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>     Fig. 3: KMovisto after importing a file

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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.

## 3.3 Molecule Changings

All changes at the molecule are made in the Molecule menu. Select the Atoms submenu for changing atom properties. The following dialog box appears (Fig. 4):

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>     Fig. 4: Dialog box for changing atom parameters

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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 chapter 4.5 for further informations.

To change the bond properties you should select the Bonds submenu. (Fig. 5).

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>     Fig. 5: Dialog box for changing bond parameters

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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 chapter 4.5. 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 chapter 3.4.

The next submenu called Molecule->Appearance is usefull to to adapt the look of the molecule in KMovisto (Fig. 6).

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>     Fig. 6: Dialog box for changing the appearance of the molecule

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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 Background Color 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.

At least, you maybe want to change the document title. Use the Molecule->Title submenu (Fig. 7) for this purpose.

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>     Fig. 7: Dialog box for changing the title of the molecule

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## 3.4 Export Files

Now you are able to export the molecule data. To do this use the File->Export submenu, select an export format or press the corresponding export button (yellow arrows up) from the toolbar (POV-Ray, VRML or XYZ format) and define a filename (see Fig. 2 in chapter 3.2.

To define your individual POV-Ray settings choose POV-Ray from the Preferences menu. Select one of the tab sheets to change parameters. The Atoms (Fig. 8) sheet allows to set parameters for drawing atoms as texture, atom color and atom size.

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>     Fig. 8: Dialog box for changing POV-Ray atom parameters

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The second tab sheet (Fig. 9) 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.

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>     Fig. 9: Dialog box for changing POV-Ray bond parameters

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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 Fig. 10 shows the third tab sheet makes it possible for you to define up to three light sources and enable or disable the Shadowless option.

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>     Fig. 10: Dialog box for changing POV-Ray light parameters

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To adjust the camera position and settings use the last tab sheet named camera (Fig. 11). Right and Up 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. Direction means the direction of the camera. It is recommended to use the same view direction as KMovisto does, so take the default value. The Location 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 Look At vector defines the origin.

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>     Fig. 11: Dialog box for changing POV-Ray camera parameters

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With KMovisto you are able to export VRML files too. To define your individual VRML settings choose VRML from the Preferences menu. The first tab sheet named Atoms (Fig. 12) is for setting an alternate atom color and atom radius.

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>     Fig. 12: Dialog box for changing VRML atom parameters

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You also want to change the bond parameters in your VRML sceene. To do this use the following tab sheet named Bonds (Fig. 13). In this tab sheet you are able to change the bond radii and define an alternate bond color.

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>     Fig. 13: Dialog box for changing VRML bond parameters

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The third and last tab sheet of the Appearance->VRML dialog named Appearance (Fig. 14) 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.

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>     Fig. 14: Dialog box for changing VRML appearance parameters

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To simplify the work with KMovisto, the dialog Directories (Fig. 15) found at Preferences->Directories 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 chapter 6.

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>     Fig. 15: Dialog box for changing working directories

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