6.33. Winmostar Viewer

Winmostar Viewer is software attached to Winmostar specialized for drawing, displaying molecular orbital etc.
It is also possible to display only specific ingredients in a multicomponent system like MD.

6.33.1. How to use the mouse

Left button + drag
Rotate the viewpoint.
As you drag and release the mouse button it will continue to rotate.
Right button + up and down drag Zoom In/Out.
Left button + right button + drag It moves vertically and horizontally.

6.33.2. Menu operation

6.33.2.1. File menu

Open
Read gld and MOLDA format files.
Save GLD
Save the currently open GLD format file with a name.
Save MOLDA
Save the structure displayed in the window in MOLDA format.
Save JPEG
Save the contents displayed in the window as a JPEG file.
Save JPEG (Stereo)
Save the left and right screens for stereoscopic viewing as a JPEG file.
StereoPhoto Maker
Start StereoPhotomaker.
Exit
Quit Winmsotar Viewer.

6.33.2.2. View menu

Representations
Perform detailed drawing adjustment Representations window is displayed.
Perspective
I use perspective.
Background Color

Specify the color of the background.

Winmostar Viewer
Make the background color dark blue.
Winmostar
Make the background color the default background color of Winmostar.
Black
Make the background color black.
White
Set the background color to white.
Model

Select the model to display.

Ball-and-Stick Model
Display the spherical bar model.
Space-Filling Model
Display space filling model.
Stick Model
Displays the bar model.
Wire Model
Display wire model.
Show SPace-Filling Model Overlapping
Display superimposed spatial priority models translucently.
Show Animation Control Panel
Animation operation panel is displayed.
Copy Image
Copy the image displayed in the window to the clipboard.

6.33.2.3. Help menu

Help
It shows how to use the mouse.
About Winmostar Viewer
Display version.
Debug
Displays debugging information such as memory usage.

6.33.3. Animation operation panel

When you display animation in Winmostar 3D, the UI for animation operation appears in the upper left corner of Winmostar 3D window.

slider
Move the frame.
Once
When playback reaches the last frame, playback stops.
Loop
When playback reaches the last frame, return to the first frame and repeat playback.
Round
Repeat playback in round trip.
JPEG
When playing with checked, the displayed contents are saved in JPEG format
GIF
When you play with the checked, the displayed contents are saved in GIF format
Close
Close this panel.

6.33.4. Representations window

Orbit/Rotation

Specify the rotation method when rotating the viewpoint with left drag.

Orbit
Rotate freely.
X, Y or Z
Rotate around the horizontal direction within the window, the vertical direction within the screen, or the direction perpendicular to the screen.
Periodic Boundary Condition

Specify how to display molecules that are outside the cell.

None
Display the original coordinates as they are.
Atom
It displays the structure so that it fits within the cell in atomic units.
Mol
Displays the structure so that the structure fits within the cell in molecule units.
Molecule
From the 1 in the middle of this window 9 is assigned to each molecule.
Composition
Assign 9 from 1 in the middle of this window to each molecular species (with the same molecular weight).
1 - 9
The checked items are displayed. In the pull-down menu BS, SF, ST, WI are Ball-stick model (default), Space filling , Stick (rod) model, wire model.
Rainbow
It displays in different colors for each molecule.
Gold
The molecule is displayed in gold color.
Stereo
It displays stereoscopically.
Enantiomer
Display the original structure and its mirror image.
Para
Display in parallel method.
Cross
It displays by the intersection method.
Anag
It displays with anaglyph. (Red and blue glasses are used)
Shift
Specify the distance between molecules.
red
Specify the size of the molecule to rotate.
H
If checked, hydrogen atoms are displayed.
Dummy
When checked, dummy atoms are displayed.
Backbone
If checked, only the backbone will be displayed. (For proteins)
Atom
Sets the display magnification of atoms.
Bond
Sets the display magnification of the join.
Z-Clip
Specify the clipping position in the Z direction.
Surface Style

Specify how to display isosurface such as molecular orbital.

Mesh
We display the isosurface in mesh (lattice) model.
Solid
Displays the isosurface in a solid model.
SmoothSolid
Display the isosurface in a smooth solid model.
Trans
Specify the transparency of the isosurface. (0: opaque, 1: transparent)
X, Y, Z
When mesh (scalar field) information such as molecular orbital is read, draw contour map (contour line) against the checked surface. The position of the contour map can be adjusted with the slider.