The Main Window

The programme displays the molecule according to the coordinates in the main window. Following manipulations are possible:

• Holding down the left mouse button and moving the mouse horizontally
  This rotates the molecule or a light source around the y axis.
• Holding down the left mouse button and moving the mouse vertically
  This rotates the molecule or a light source around the x axis.
• Holding down the middle mouse button and moving the mouse horizontally
  This rotates the molecule or a light source around the z axis.

  All rotations are carried out in a molecule fixed coordinate system.

• Holding down one of the shift keys and the left mouse button and moving the mouse
  This moves the molecule.
• Holding down one of the shift keys and the middle button and moving the mouse
  The scaling of the molecule is changed.
• Pressing the cursor keys for moving up or down
  The scaling of the molecule is changed. By pressing the molecule will be enlarged and by pressing the molecule will be made smaller.
• Clicking on an atom with the left mouse button
  This selects this atom, you will hear a beep. If you have clicked on one atom and then pressed the right mouse button, the average of all bond lengths at this atom is displayed. If you have clicked on two atoms and then pressed the right mouse button, the distance between these two atoms is displayed. If you have clicked on three atoms and then pressed the right mouse button, the angle between these three atoms is displayed. If you have clicked on four atoms and then pressed the right mouse button, the torsion angle between these four atoms is displayed. To delete the displayed values use either the Geometry menu items or repeat the steps above. Clicking with the left mouse button on an atom may be also necessary for setting or selecting some atom specific values (vide infra).
• Pressing the right mouse button without clicking on an atom before
  A menu will appear. The menu contains the following topics (the key combination in parantheses can be used as a shortcut in the English version):
  • Wire model (Alt+W)
    The molecule will be drawn with lines. This is the default.
  • Stick model (Alt+T)
    The molecule will be drawn with sticks.
  • Ball and stick model (Alt+A)
    The molecule will be drawn with balls and sticks.
  • CPK model (Alt+C)
    The molecule will be drawn with cups.
  • Geometry
    A submenu is provided with the following topics:
    • Clear all (Ctrl+A)
      If this topic is selected all bond lengths, bond angles, and torsion angles currently labelled with its value are deleted.
    • Clear last (Ctrl+L)
      If this topic is selected the last bond length, bond angle, and torsion angle, respectively, labelled with its value is deleted.
  • Wave function ... (Alt+V)
    The dialogue box shown in Figure 1 is presented. This topic is currently only available with TURBOMOLE and GAUSSIAN outputs, and even then only if MO coefficients and basis functions could be read in and if the calculation was closed shell. If TURBOMOLE output is used and the point group of the molecule in $symmetry is not C$$₁, TURBOMOLE's moloch programme must be available (vide supra, p. ) and only basis functions, occupied MO's, and electron densities can be drawn in this case. Since TURBOMOLE can handle up to g functions and GAUSSIAN can handle up to f functions the same limitations apply to VIEWMOL.

    If any wave function related drawing is displayed and the grid granularity is changed the drawing disappears and the recalculation has to be explicitly demanded by selecting this menu item again, since large molecules require significant time for the recalculation.

     
    Figure 1:  The dialogue box for setting options for wave function related topics.
    

    At the top of this dialogue box are five buttons which can be used to select the property which shall be shown.

    • All off
      This topic disables the drawing of any wave function related topic. This is the default.
    • Basis function
      This topic allows drawing of basis functions. After selecting it and closing the wave function dialogue VIEWMOL prompts for an atom in its main window. Clicking on an atom with the left mouse button will present a dialog box with all basis functions centered on this atom. After selecting one of this basis functions and pressing the OK button the corresponding basis function will be drawn.
    • Basis function in MO
      This topic allows drawing of basis functions multiplied by the corresponding coefficient in a molecular orbital. This topic works similiar to the previous one, except that the menu will show the MO coefficients in front of all basis functions. This topic is only selectable if a molecular orbital has been selected in the MO energy diagram window.
    • Molecular orbital
      This topic allows the drawing of a molecular orbital. It is only selectable if a molecular orbital has been selected in the MO energy diagram window.
    • Electron density
      This topic allows the drawing of the total electron density.
    Next to these buttons there is a slider which can be used to select the value of the isosurface used to draw the property selected. Following this slider another three buttons allow the selection of the interpolation method used in drawing the property.
    • None
      No interpolation is done. The resulting drawing normally has a lot of edges.
    • Linear
      A linear interpolation is done between grid points. This gives a much smoother surface.
    • Logarithmic
      A logarithmic interpolation is done between grid points. This improves the quality of drawing further.
    The default is linear, but this can be overwritten in the resource file (vide infra, p. ). At the bottom of the dialogue box there is another slider with can be used to set the granularity of the grid. As higher the number selected here as finer the grid and as smoother the resulting surface, but the calculation time goes with the third power of this number. Default is 10, but this can be overwritten in the resource file (vide infra, p. ).
  • Energy level diagram (Alt+E)
    A new window will appear which shows the calculated energies of the MOs in an energy level diagram. This topic is only available using DMOL, GAUSSIAN 9X, or TURBOMOLE outputs. In TURBOMOLE outputs the data group $scfmo must be available.
  • Optimization history (Alt+O)
    A diagram is plotted in a second window which shows the energies and gradient norms of the geometry optimization. With the cursor keys for moving to the left and to the right one can see how the geometry optimization works. Alternatively, the red cross can be dragged with the mouse.
  • Show forces (Alt+F)
    The calculated forces acting on the atoms are drawn as arrows. This topic is not available using DISCOVER outputs. The topic is also not available, if no forces were found for the current coordinates.
  • Spectrum (Alt+S)
    A new window will appear which shows the calculated spectrum for the molecule. This topic is only available if a force constants calculation has been performed.
  • Show unit cell (Alt+N)
    The display of the unit cell is toggled. The unit cell is only available in DISCOVER and DSOLID files.
  • Show ellipsoid of inertia (Alt+I)
    The display of the ellipsoid of inertia is toggled.
  • Drawing modes (Alt+M)
    

     
    Figure 2:  The dialogue box for setting options for drawing style.
    

    The dialogue box shown in Figure 2 is provided:

    • with dots
      Drawing of sticks, balls, CPKs and/or molecular orbitals is done as a dot cloud.
    • with lines
      Drawing of sticks, balls, CPKs and/or molecular orbitals is done with meshes.
    • with surface
      Drawing of sticks, balls, CPKs and/or molecular orbitals is done with an opaque surface which has the properties defined in the viewmolrc file (these properties hold for sticks as well as for balls or CPKs).
    • Lines while rotating
      If this option is selected the drawing of the molecule will be done with lines during translations and rotations. These speeds up movements on low-end graphics systems. The default is on, but this can be changed in the resource file. (Note: If you run on Linux with Mesa, do not set this option to off. Mesa has a bug which will crash VIEWMOL if a drawing with surfaces shall be rotated.)
    • Lights on/off, Light 1
    • Lights on/off, Light 2
      These two button can be used to switch lights on and off. Lights have only an effect if the drawing mode is "with surface" and either the stick, ball-and-stick, or CPK model is selected.
    • Move light, Do not move light
    • Move light, Light 1
    • Move light, Light 2
      These items can be used to select whether the movement of the mouse in the window will effect the molecule ("Do not move light") or one of the light sources ("Light 1" or "Light 2"). If a "Light 1" or "Light 2" is selected the lights can be rotated around the molecule.
    • Resolution of spheres
      The number of polygons used for the drawing of sticks, balls and/or CPKs is changed. A higher value makes the surfaces more smoothly looking, but also decreases drawing speed. A lower value makes the surfaces rougher looking, but increases drawing speed.
    • Background colour (Alt+B)
      The colour editor appears in a seperate window which can be used to change the background colour of the window (see description of the colour editor below, p. ).
    • Label atoms (Alt+L)
      The atoms are labeled with atom symbols from input files. A number counting the atoms according to their order in the input is concatenated to the symbol.
    • Save drawing (Alt+D)
      

       
      Figure 3:  The dialogue box for setting options to save a drawing
      

        The dialog box shown in Fig. 3 is provided which can be used to set file formats, file names and other options for writing the drawing to a file.

      • TIFF
        The current drawing of the molecule is written out as a TIFF file. The "TIFF compression" menu permits the selection of a compression algorithm. If normal modes are animated while this option is selected a series of 24 TIFF files will be written out, each contains a single frame of the animation. By using standard image manipulation tools available on the Internet it is possible to generate a video file (MPEG) from these TIFF files which can be included in multimedia documents (vide infra, p. ).
      • HPGL
        The current drawing of the molecule is written out as a HPGL file for plotting on a plotter or a laser printer. This topic is not available if the drawing is done with sticks, balls, or cups and surfaces.
      • PostScript
        The current drawing of the molecule is written out as a PostScript file. This topic is not available if the drawing is done with sticks, balls, or cups and surfaces.
      • Rayshade
        The current drawing of the molecule is written out as an input file for RAYSHADE. This topic is only available if the drawing is done with sticks, balls, or cups. If molecular orbitals are drawn this topic is only available if the MO is drawn with a surface. If normal modes are animated while this option is selected a series of 24 input files for RAYSHADE will be written out, each containing a single frame of the animation.
      • Landscape
      • Portrait
        The orientation of the drawing on the page can be chosen if the drawing is written out as either a HPGL or a Postscript file.
      • TIFF compression
        Can be used to select the compression mode for TIFF files. Due to a software patent on the LZW compression algorithm this compression can no longer be provided.
      • File
        The name for the file to be generated.
      • Select
        Brings up a file selection box to select the name for the file to be generated.
      • Paper size
        Can be used to select the paper size.
      • Paper width in mm
      • Paper height in mm
        Input user defined paper width and height. Only available if "Paper size" is set to "User defined".
    • Help/Manual (Alt+H)
      This topic opens a window with the VIEWMOL manual. This topic is only available if the file viewmol.html was found in the location $VIEWMOLPATH/man.
    • Save molecule
      The current geometry of the molecule is written to a file in TURBOMOLE format.
    • Quit Viewmol (Q)
      This quits the programme.