- Molecule ...
A submenu is provided with the following topics:
- Load molecule ...
Brings up a file selection box to load a molecule. - Save molecule ...
Brings up a format selection dialog and a file selection box to
save the currently selected molecule to file. Output formats are
supported through external filters (similar to the input filters) and can
be installed using options in the viewmolrc
file (cf. p.
).
Coordinates and bond information are passed to the corresponding output filter which
writes the file. Currently, the only output formats provided are MSI car-files,
MDL mol-files, and TURBOMOLE. - Delete molecule ...
Deletes the currently selected molecule. - New molecule ...
Brings up the molecule editor and starts the building of a new molecule (cf. p.
). - Modify molecule ...
Brings up the molecule editor to modify an existing molecule (cf. p.
).
- Select molecule
Provides a submenu with the names of all molecules currently loaded
and an item All
and can be used to change the currently
selected molecule. Other possibilities to select a molecule consist
of clicking on the molecule (preferably while holding the shift key down)
or pressing the Tab
key, which cycles through all entries in the
Select molecule
submenu. - 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 CPKs. - Geometry ...
A submenu is provided with the following topics:
- Clear all (Ctrl+A)
If this topic is selected all labels of bond lengths, bond angles, and torsion
angles are deleted. - Clear last (Ctrl+L)
If this topic is selected the label of a bond length, bond angle, or torsion
angle created last is deleted. - Undo geometry change (Ctrl+U)
If this topic is selected, the last geometry change (cf. p.
) is
reversed. All geometry changes are buffered in the undo buffer and can be reversed one
by one by repeatedly using this menu item. Geometry changes can also be reversed through
the molecule editor.
Figure 2: The dialog box for setting options for
bonds.
- Bond types ...
Brings up the dialog box shown in the Figure.
- single only
All bonds are drawn as single bonds. - multiple
VIEWMOL determines the bond order for each bond considering connectivity
and elements only (only the following elements are used in the determination
of bond orders: H, C, N, O, F, Si, P, S, Cl, Ge, Br, I). VIEWMOL then
draws bonds with the corresponding bond order. Bond orders can also be changed
in the molecule editor. - conjugated
VIEWMOL determines bond orders as for the "multiple" option. It then
determines whether multiple bonds are conjugated and draws them as such.
This is the default, but can be overwritten using resources (see p.
). - Show hydrogen bonds
This button toggles the display of hydrogen bonds. Hydrogen bonds are determined
automatically by VIEWMOL based on a distance threshold. - Threshold for hydrogen bonds [Ang]
This slider can be used to set the distance threshold for the automatic determination
of hydrogen bonds. A hydrogen bond is shown if the distance between a hydrogen atom
and another atom is larger than the sum of their radii, but smaller than this
threshold. The default is 2 Å.
- Scale radius for all atoms by
This menu and the slider beneath it can be used to scale the Van der Waals
radius for an element. Since the Van der Waals radius determines the connectivity
of the atoms in the molecule, changing it will also change the connectivity. The
option menu can be used to select which element to scale and the slider allows
to set the scaling factor.
- Wave function ... (Alt+V)
The dialog box shown in the Figure
is presented. This topic is currently only available with TURBOMOLE, GAUSSIAN, and MOPAC 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, TURBOMOLE's moloch program 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 resolution
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 3: The dialog box for setting options for
wave function related topics.
At the top of this dialog 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 dialog 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 similar to the previous
one, except that the menu will show the MO coefficients in front of all basis
functions. If no molecular orbital has been selected in the MO energy diagram
window a warning message will be displayed. - Molecular orbital
This topic allows the drawing of a molecular orbital. If no molecular orbital
has been selected in the MO energy diagram window a warning message will be
displayed. - 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.
). Following is another
slider with can be used to set the resolution 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.
). At the bottom of the dialog box is a toggle button
which can be used to turn automatic recalculation of MOs etc. on whenever the
energy level is changed. Since these calculations can be quite time consuming,
this button is off by default, 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, MOPAC, 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. - Unit cell (Alt+N)
Figure 4: The dialog box for modifying the unit
cell.
The dialog box shown in the Figure
is displayed. The first button, visible
, allows to turn the
display of the unit cell on or off. The three sliders can be used to increase
or decrease the number of unit cells displayed in each crystallographic
direction. By default between one and five unit cells can be selected.
- Show ellipsoid of inertia (Alt+I)
The display of the ellipsoid of inertia is toggled. - Drawing modes ... (Alt+M)
Figure 5: The dialog box for setting options for
drawing style.
The dialog box shown in the Figure
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. This speeds up movements on
low-end graphics systems. The default is on, but this can be changed in
the resource file. - Orthographic projection
The molecule is drawn using an orthographic projection. - Perspective projection
The molecule is drawn using a perspective projection. This kind of projection
resembles more closely the way the human eye perceives things. - Move molecule
If this button is selected all translations and rotations carried out with
the mouse act on the currently selected molecule. - Move view point
If this button is selected all translations and rotations carried out with
the mouse act on the viewpoint. This option is only available if perspective
projection is used. Moving the view point allows the user to move into a
molecule. - Move light 1
If this button is selected all translations and rotations carried out with
the mouse act on light 1. - Move light 2
If this button is selected all translations and rotations carried out with
the mouse act on light 2. - 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. - 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. - Line width
The line width used for drawing the molecule as wire frame model can be
selected. A value of 0 means dynamic determination of the line width based
on the size of the window. This value is the default.
- Ground color (Alt+G)
The color editor appears in a separate window which can be used
to change the color of the ground if perspective drawing is enabled
(see description of the color editor below, p.
). - Background color (Alt+B)
The color editor appears in a separate window which can be used
to change the background color of the window (see description
of the color 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. - Annotate (Ctrl+N)
Using this topic annotations can be created in the main window. After selecting
this topic the cursor turns into a text input cursor. Clicking at any point
in the main window now allows to enter an arbitrary text string. Pressing
return ends the annotation function. Existing annotations can be edited
by simply clicking on them or deleted by deleting all characters in the string.
Annotations can be moved in the same way as the molecule can be moved: hold
a shift key down, click on the annotation and move the mouse. Annotations
support the clipboard, i. e. annotations can be cut and pasted between applications. - Save drawing (Alt+D)
Figure 6: The dialog box for setting options to save a drawing
The dialog box shown in the Figure 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 20 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 CPKs and surfaces. - PostScript
The current drawing of the molecule is written out as a PostScript file. If this
topic is selected while the drawing is done with sticks, balls, or CPKs and
surfaces a resolution independent PostScript file for the drawing is written,
but since PostScript does not provide a way to automatically remove hidden
surfaces the drawing may contain some artifacts. The algorithm used tries
to minimize these artifacts, but is not always completely successful.
Sometimes changing the orientation of the molecule slightly or increasing the
resolution of the spheres might help. - 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 CPKs. 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 20 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
. - Configuration ...
Figure 7: The dialog box for setting configuration
options.
The dialog box shown in the Figure
is provided. At the top of this dialog the language VIEWMOL uses in its
interface can be selected. VIEWMOL loads its language specific data from
files Xdefaults.<language>
from the directory VIEWMOLAPATH
points
to. The four text input fields can be used to specify the location of helper
programs VIEWMOL needs for some of its operations. If the corresponding
program was found in the path the dialog box will already show the correct
information. If the programs specified here need file names as parameters, put
%s
as a place holder for the file name in the command.
A the bottom is a button Save
which allows the information entered in
this dialog as well as some other settings to be stored as resources in
$HOME/.Xdefaults
. The following settings are saved: position and
size of all open windows, window colors, selected model, selected drawing
mode, selected bond type, setting of "lines while rotating", selected
interpolation mode, resolution of spheres, line width, selected isosurface,
selected resolution for density of states, setting of "automatic recalculation",
paper size, and hydrogen bond threshold. Note: On Linux
the setting of resources is kept across different invocations of the
program. Saving the configuration and restarting VIEWMOL will
therefore apparently not work. To get rid of the old resource settings
issue the command xrdb -remove $HOME/.Xdefaults
or log out and
in again.
- Quit Viewmol (Q)
This quits the program.