Perform Basic Operations

Data Panel To show the data panel for a calculation attribute or property, click on the item's button. Scene Viewer To enable the display of attribute or property data in the scene viewer, click on the corresponding scene viewer button.

View/Print/Export Property Data

To view the data panel for a calculation property, click on the property's button. The property data are displayed in the current display mode (either a graphic plot or a table). If the calculation is still running, the property values will be updated as results become available.

Picture...

Plot and Table Examples

To switch between a table and a plot:

1. Position the mouse cursor over the property data panel, and click the right mouse button, or click the Options button, if available (for example, Geometry Trace and Normal Modes have the Options button).

   This opens a pop-up menu for choosing the display mode. The menu may also contain other display options. Examples:

   Plot Pop-Up Menu		Table Pop-Up Menu

2. Then ...
   • To display a table, mark the Table View option.
     OR
   • To display a plot, unmark the Table View option.

   Both versions of the menu include a Print option. The table menu includes an Export option for saving table files in ASCII text format or in SYLK spreadsheet format.

Manipulate Data Plots

If a property plot contains a large number of data points, it may be helpful to zoom in on a subset of the data or change the type of graph scale.

How to...	Instructions
View data values	Click on any data point (). The property value displays above or below the data point.
View linear or log scales	You can view the graph using a linear scale, a log scale if the values are positive numbers or a log scale using the absolute value if the data contains negative but non-zero numbers. 1. Click on the down arrow in the corner of the property plot. 2. Select Linear Scale or Log (absolute) Scale The selected scale will display on the graph.
Zoom in on a subset	1. Position the cursor at one corner of the desired area. Hold down Ctrl +  together and move the cursor in any direction. A rectangle forms with a one corner fixed where you started and the opposite corner following the cursor. 2. Release the mouse button to complete the selection. This expands the enclosed portion of the plot to fill the plot area. 3. Press the r key to return to the default view.
Shift (translate) the plot	Hold down Shift +  together and drag the plot in any direction. This shifts the plot within the plot area.
Scale the size of the plot	Hold down Ctrl +  together and move the mouse up or down. "Up" enlarges the plot. "Down" shrinks the plot.
Return to default display	Press the "r" key. All zooming, translation, and scaling is removed.

Customize How Chemical Systems are Displayed

Use the Details: ChemSys Display Options window to adjust the appearance of atoms and bonds. The visible effect of the window controls depends on the general display style already in effect (Ball & Stick, Stick, Ball & Wireframe, Stick, Wireframe, or CPK).

1. From the Builder's Display menu or the Calculation Viewer's Chemical System menu, choose Render Quality and then Customize.

   The resulting options window displays the current settings and controls. All controls in the window are either exclusive options or range sliders. Most sliders are marked from 1 to 100% with corresponding dynamic readouts from .01 to 1.0 .

2. To adjust a display attribute, mark the option box or drag the range slider using the left mouse button.

   Wire Options (chemical system appearance for Wireframe styles)
   Line Width	Width of the lines used for wireframe from about 1 to 10 pixels (.01 to .10).
   Cylinder Options (bond appearance for Stick styles)
   Cap Style	Appearance of the atom ends of the bonds (Caps appear only in Stick style.)
   Render Quality	The stick quality modifies the stick cross section from nearly triangular (0.1) to circular (1.0).
   Radius	Radius of sticks
   Sphere Options (atom appearance for Ball and CPK styles)
   Hemi Spheres or Full Spheres	Full Spheres is the preferred option for most workstations. The Hemi Spheres option may increase display speed, but the display can be uneven.
   Render Quality	The sphere quality modifies the rendering from an 8-faced cube (.01) to an n-faced polyhedron approximating a sphere (1.0) The default sphere quality is set at about 50% (0.5). Higher values will increase the graphic quality and rendering time for atom surfaces.
   Ball/Stick Scale	Relative size of the spheres from near zero (.01) to normal (1.0)

Select Atoms and Residues by Radius

Use the Edit: Select Within Radius window to select all atoms or residues within a defined radius of currently selected atom(s).

Radius selection can be based on a single atom or a set (multiple atoms) of atoms. Any non-highlighted (unselected) atom that is within the specified radius of any of the highlighted atoms will be included in the radius selection results. The Select Within Radius option defines the distance, from any of the highlighted atoms, to use for the radius select search.

If Select Complete Residues is indicated, then all atoms of a residue will be included in the radius selection results if one or more of its atoms are within the specified radius.

1. Select an atom or multiple atoms in the molecule.

2. From the Builder's Edit menu or the Calculation Viewer's Edit menu, choose Select Within Radius.

   The resulting options window displays the current settings and controls.

3. Enter a radius in angstroms.

4. To select complete residues, click the Select complete residues checkbox.

5. Click the Select button to select all the atoms within the specified distance of any currently selected atoms. If the "Select complete residues" toggle is set, then all atoms in any residue that was within the specified distance will also be selected. The centers of atoms must be within the radius to be selected.

Selection Options
Radius	Select all atoms that are within the specified distance (radius) of any currently selected atom.
Select complete residues	Selects a volume encompassed by the radius you set, and will include the complete residue beyond the specified radius. All atoms in any residue that has at least one atom within the specified distance will be selected.

Manipulate Objects in the Viewer

To manipulate objects along fixed axes, use the "thumbwheel" controls.

To manipulate objects directly with the mouse:

1. Click on the Manipulate button .

   The cursor switches to the Manipulate cursor (hand) in the work area.

2. To rotate the chemical system in arbitrary directions around a center point:

   Hold down the left mouse button and drag the cursor in any direction within the scene viewer.

   To move (translate) the system in the (x,y) plane of the scene viewer:

   Hold down the middle mouse button and drag the system within the scene viewer. The cursor switches to the Translate cursor (hand with object) in the scene viewer.

   To dolly/zoom in the scene viewer:

   Hold down  left + middle mouse buttons together (or Ctrl + ) and move the cursor up or down in the scene viewer. The cursor switches to the Dolly cursor (pointing hand) in the scene viewer.

View Grids

To display 3D Gaussian Cube Formatted data files containing grid-type data for a calculation:

1. Click on the data panel and viewer buttons for Grids.

   Picture...

   Grids panel

2. Click on the Import button.

3. From the Import window, select a *.cube file from the desired directory and click Import. The 3D cube file will display, along with image data for the 3D file.
4. To visualise each grid, click on the grid name in the list.

5. To remove a particular visualization from the list, select the grid name and click the Unload button.

6. To create a new visualization, enter the names of grids in the Calculate Grid fields and click the Go button. The new visualization will display and its name will be added to the list.

Show Molecular Orbitals (MOs)

To display isosurfaces for a selected MO:

1. Click on the data panel and viewer buttons for MOs.

   Picture...

   MOs panel

2. Click on one occupied orbital (MO row) in the MO table.

3. From the menu button, choose MO.

4. Optional:

   	a. Mark the Show Coeff option to view a table of coefficients.
   	b. At the ABS > field enter a cutoff value. (Coefficients below this value are ignored in computing isosurfaces.) The cutoff value will apply to all calculations.

5. Click on the Compute button to compute the image data for that orbital.

6. Drag the Iso: slider to set the value depicted as an isosurface in the scene viewer.

Show Total Electron Density

To display isosurfaces for total electron density (all occupied orbitals):

1. Click on the data panel and viewer buttons for MOs.

   Picture...

   MOs panel

2. From the menu button, choose Density.

3. Click on the Compute button.

   A pop-up window (with a Stop button) indicates the progress of computing the display for each occupied orbital.

4. Drag the Iso: slider to set the density value depicted as an isosurface in the scene viewer.

   Picture...

   MO Isosurfaces Example

Change the 3D Grid for MO Surfaces

Use the 3D Grid Definition window to change the resolution and extent of the 3D grid that is used for calculating MO (and electron density) isosurfaces for display. For example, when viewing a large molecule, you may want to limit the display of surfaces to a particular group but increase the resolution (and quality) of the surfaces.

Picture...

3D Grid Definition Window

1. From the Calculation Viewer's Surface menu, choose Define Grid.

   The resulting 3D Grid Definition window usually includes default values for the current chemical system--a reasonable resolution and an extent that includes the entire chemical system.

2. To adjust the grid resolution (number of values along each dimension XYZ), type a new value in the X=Y=Z field.

   Increasing the resolution means higher-quality surfaces but a longer time needed to compute them.

   By default, the resolution is uniform--the same along each dimension. If you want to exaggerate a surface effect, unmark the Uniform option. This enables the individual Res: fields so that you can type a separate resolution value for each dimension XYZ.

3. To adjust the grid extent (limits of each dimension), type new From: and To: values for each dimension XYZ.

   MO and electron density isosurface values will be computed only for nodes that are within the specified grid volume.

4. To see the results of changes to the 3D grid for either MOs or total electron density, click on the Compute button in the MO data panel.

Show a Geometry Trace Animation

1. Click on the data panel and viewer buttons for Geometry Trace.

   Picture...

   Geometry Trace panel

   Tip: To use the geometry end state of a calculation as the starting state of another, use the "drag site" in the corner of the Geometry Trace panel. Drag the chemical system--and its geometry from the final step of a completed geometry optimization--to a calculation in the Calculation Manager.

2. 		Click on the forward or backward buttons to show the chemical system image at each geometry step.
   		Or click on the loop button to show the geometry trace animation continously.

   The corresponding value in the graphic plot (or table) is highlighted at each geometry step.

• To change the speed of the animation, modify the Delay (the interval between the frame steps of the animated sequence).
  
  
• To view XYZ coordinates for the currently displayed step, click on the XYZ button.

Show Normal Modes Animation

1. Click on the data panel and viewer buttons for Normal Modes.

   Picture...

   Normal Modes panel

2. Select a normal mode frequency (table row).

3. Mark the Animation Display option.

4. Click on the loop button to show the normal modes animation.

• To change the speed of the animation, modify the Delay (the interval between the frame steps of the animated sequence).
  
  
• To change the quality of the animation, modify the # Animations (the number of frame steps in one animation loop).
  
  
• To scale the amplitude of the normal mode displacement, drag the Scale slider above the viewer. The scale factor is the value by which the normal mode displacement is multiplied. The initial value is set to 1. To reset the slider to 1 after adjustment, you may need to click on the slider background, or display another property and then return to normal modes.
  
  
• To view a representation of normal mode vectors, mark the Vector Display option. Vectors are represented by 3D arrows. (Vector Display is selectable only when the animation is stopped.)
  
  
• To change the direction of the displacement, click on the Swap Sign of Displacement toggle button. The normal mode displacement is either added or subtracted from the atomic coordinates. The effect is to change the vector direction or the initial animation direction.
  
  
• To force all animation steps in the same direction, mark the Actual Displacement option. This allows you to produce geometries along a vibration mode displaced by a specific number of steps.

  Tip: To capture the displaced geometry for a new calculation, use the "drag site" in the Normal Modes panel. Stop the normal modes animation at the desired step, and then drag the chemical system from the drag site to a calculation in the Calculation Manager. This may be useful when applied to an imaginary frequency obtained during geometry minimization. By stopping the animation at a displaced geometry, you can start a new geometry optimization from the distorted structure, which may actually converge to a minimum energy structure.

Show Mulliken Charges

1. Click on the data panel and viewer buttons for Mulliken Charges.

   Picture...

   Mulliken Charges panel

2. To display the Mulliken charge associated with an atom, click on an atom from the list. In the scene viewer, the atom will display a color corresponding to its charge. To see all combined charges for an atom, click the button next to the atom's number to display a drop-down list of all associated charges.
3. Click on another atom to display its corresponding Mulliken charge color. Colors map to the strength of the charge as indicated in the color key at the top of the data panel.

Export/Capture/Print the Viewer Image

You can export chemical structure files or graphic files from the Calculation Viewer. To export the current viewer contents:

1. From the Calculation Viewer's Calculation menu choose Export.
   
   This opens the Export dialog window.

Picture...

Export Dialog Window

2. From the Format menu, choose the desired format.
   
   Note that the export formats include graphical formats (POV-Ray, Postscript, RGB, GIF, TIFF, and JPEG) in addition to the molecular structure formats.

   POV-Ray export offers a number of options to control the appearance of the output image.

   Finish	Bonds
   Plastic Soft Metallic Wood	Bicolor-Proportional Bicolor-Symmetric Brass
   Isosurfaces	Preview - Display Size
   Glassy Soft	Picture... POV-Ray Export

   
   
3. Optional: At the end of the Filter string, type a filter for limiting the files that will be displayed in the Files list. Then press Enter (or click on the Filter button)
   
   
4. In the Directories list, click on the appropriate target directory.
   
   
5. In the Selection box, type (or edit) the name of the export file.
   
   
6. Click on the Save button.

To capture a sequence of images in the current scene viewer:

1. From the Calculation menu, choose Image Capture.

   This opens the Image Capture dialog window.

2. In the Directories list, enter the appropriate target directory for storing the captured images (/tmp is the default).

3. In the window's Prefix field, enter the prefix file name you want for your captured images. The default prefix file name is img. Captured images will be saved to sequentially numbered file names, for example, img_1.rgb, imb_2.rgb, etc.
   
4. From the window's Format pull-down menu, choose the desired image format.

   The image formats are ( POV-Ray, Postscript, RGB, GIF, TIFF, and JPEG).

5. From the window's Size pull-down menu, choose the desired image size format.

   The size formats are (Video and Viewer).

   Tip...	To use the equipment available in the EMSL Graphics and Visualization Lab, select RGB files with the size option set to Video.
   Tip...	You can specify width and height of each frame (in pixels). This capability can be used to create a set of small GIF files that can then be readily converted to an animated GIF for web page content.

   
   

6. Select the capture Mode (Real-Time or Sequence).

7. Click on the Active button to begin saving a sequence of images.
   
   As images are captured, you will see their filenames display in the Active field. Once you have clicked the Active button, the system will continue to save images until you click it again to stop. This means you can maximize the viewer window and click the Close button on the Image Capture window, capture images, then reopen the Image Capture window and click the Active button to stop capturing. This enables you to capture full-screen images without the Image Capture window being in the way of your view.
   
   
8. Click on the Active button to stop saving images.

To print the current viewer image:

1. From the Calculation menu, choose Print.

2. In the resulting Print window, select a printer from the scrolling list of available printers.

3. Click on the window's Print button.

View Calculation Input/Output Files

To view the calculation input file: From the Calculation menu, choose View Input File.

To view the calculation output file:

1. From the Calculation menu, choose View Output File.

   The output file is then shown (if one exists) in a separate monitor window. If the calculation is still running, the current bottom of the output file will be displayed (equivalent to giving a "tail -f" UNIX command).

2. If prompted to do so, press the Return (Enter) key to be able to view and scroll the information.