C637:  Introduction to Cerius² Software

Before you start the tutorial, please read the Cerius² application note which outline the Cerius² software. You may consult this note and the Cerius² manual (located in room A414, also available online on the MSI web site) during the tutorial. This tutorial deals only with the visualization related parts of the Cerius² software. You are also encouraged to go through the Cerius² Basic Tutorials on the MSI web site (contact the MolViz staff for user ID & password). A local copy of the tutorials is also accessible for the departmental SGI computers.

• Format of this document
• Getting started
• Loading a molecular model
• Moving a model
• Selecting atoms
• Displaying and coloring atoms
• Labeling atoms
• Changing the display style
• Geometry analysis
  • Measuring distances, angles, torsion angles, etc.
  • Calculating close contacts
• Others
  • Changing crystallographic display range
  • Stereo view
  • Function keys

• Menus and sub-menus are described as main menu / sub-menu e.g., File/Load Model specifies the Load Model menu under the File pull-down in the menu bar.
• All mouse-accessible selections are made by positioning the mouse cursor and clicking the LEFT mouse button.
• Keys that must be pressed simultaneously, or function keys, are listed in "<>" (e.g., <control-D> or <F9>).
• Some images and contents in this document came from the MSI's Cerius² documents.

1. Log onto a departmental SGI workstation.
2. Open a UNIX shell (click on Desktop/Unix Shell in the toolchest) and cd to the appropriate directory.
3. Type cerius2 to start the program. 
4. Take a few minutes to familiarize yourself with the layout of the Cerius² program. See the Outline of Cerius² section of the Cerius² application note.
5. To quit from the program, click on File/Exit, then confirm that you want to exit.

1. Download the REBNOB01.dat file from this web site if you don't have your own files.
2. Start Cerius² if it isn't started (see above).
3. Select File/Load Model to open the Load Model control panel:

4. Set the File Format popup to CAMBRIDGE: click on the button under File Format and keep the mouse button pressed, position the cursor on CAMBRIDGE in the popup and release the mouse button.
5. If you started Cerius² from the directory where the REBNOB01.dat file (or your own FDAT file) is stored, the REBNOB01.dat file (or your own FDAT file) will appear in the File selection list box. If not, change to that directory using the Directory selection popup and the File selection list box.
6. Click the REBNOB01.dat filename in the File selection list box then hit LOAD (or double-click the filename) to load the file. The molecular structure will be displayed in the Model window (note: for the FDAT format file, entire crystallographic unit-cell contents will be displayed).

With the cursor in the model window, you can rotate and translate models using mouse and/or keyboard:

• To rotate the models about the x or y axes, press the right mouse button and move the mouse vertically or horizontally in the central area of the model window, respectively.
• To rotate the models about the z axis (the axis perpendicular to the screen), press the right mouse button and move the mouse horizontally or vertically near an edge of the model window.
• To translate the models, press the middle mouse button and drag the mouse in any direction within the xy plane.
• To zoom in and out, press the middle and right mouse buttons (or hold down <Shift> plus the middle mouse button) and drag the cursor in the model window.
• To center the models, select View/Center in the main control panel.
• To reset the view of the models, hit on the toolbar.

• Press the up or down arrow keys to rotate the models by 45° about the x axis, and press the right or left arrow keys to rotate the models by 45° about the y axis.
• Press <End> (or <Alt> w) to scale the models to fill the model window.
• Press <F2> to enlarge the model window to full screen. Pressing <F2> again will return the model window to its usual size.
• Press <Alt> t to center the models.
• Press <Home> (or <Alt> r) to reset the view of the models.

Atoms can be selected individually or according to some criterion, such as a common property or their membership in a group. The Edit pull-down menu offers several ways of selecting one or more atoms. There are also four atom selection tools in the toolbar:

Always use the left mouse button to select atoms in the model window. You can select one atom at a time:

• To select an atom, click that atom. The selection is conformed by a beep, and the atom is highlighted.
• Clicking another atom will select the new atom and deselect all others.
• To select additional atoms, hold down <Shift> and click one or more atoms.
• To deselect an already selected atom, <Shift>-click that atom.

• Hold down the left mouse button and drag out a rectangle in the model window so as to enclose several atoms. The atoms in the rectangle are selected.
• Drag out another rectangle to select a different group of atoms (or one atom) and deselect all others.
• <Shift>-drag to select an additional group of atoms.
• <Shift>-drag some already selected atoms to deselect them.

• Click on the toolbar to select all atoms.
• Click on the toolbar (or click in empty space in the model window) to deselect all atoms.

1. Click View/Atom Visibility to popup the Atom Visibility control panel.
2. Check Hide Hydrogen Atoms on the control panel to remove all hydrogen atoms from the display.
3. Check Show All Atoms on the control panel to display all atoms.

4. Click View/Colors to access the Color Selected Objects control panel.
5. Select the atoms that you want to color, and choose the desired property (e.g., Charge) from the Color by a Property list in the Color Selected Objects control panel.
6. To return the selected atoms to their default element colors, click the Reset selected object colors to default button in the Color Selected Objects control panel.

7. On the Color Selected Objects control panel, choose a color (e.g., red) from the Pen popup.
8. Set the Pen popup to DEFAULT to return the selected atoms to their default element colors.

Atoms can be labeled according to various properties:  element types (ELEMENTS), atom partial charges (CHARGES), atom formal charges (FORMAL CHARGE), atom serial numbers (NUMBERS), atom site occupancies (OCCUPANCY), atom isotropic temperature factors (ISOTROPIC), forcefield atom types (FFYTPE), atom hybridization (HYBRID), atom name (NAME), atom mass (MASS), and crystal symmetry copy plus atom serial numbers (SYM/NUM). The default is NO LABEL. Labels can be applied to entire models (when all or no atoms are selected) or to selected atoms within one or more models. Different labels may be used for different parts of a model.

• Use the label popup menu on the toolbar to label atoms with the desired property (or NO LABEL). For example, set the label popup to ELEMENTS, then to NUMBERS, and finally back to NO LABEL.

The default display style of the models is STICK. In this style, bonds are displayed as single, double, or triple lines. Atoms are not shown, but implied at the ends of bonds. The bond colors represent the element types of the atoms at each end. The other display styles, including BALL (atoms as balls), CYLINDER (bonds as cylinders), BALL & STICK, ELLIPSOID, POLYHEDRA (cations as polyhedra), and TRACE , can also be chosen for presenting the models. The display styles can be applied to entire models (when all or no atoms are selected) or to selected atoms within one or more models. Different display styles may be used for different parts of a model.

1. Use the display style popup menu on the toolbar to specify the display style. Try setting the display style to BALL, STICK and CYLINDER, then back to STICK.

2. Alternatively, you can change the display style using the menu bar. In this way, you can also set the style preferences (e.g., ball size, cylinder radius, resolution, etc.).
   • Click View/Display Attributes... in the menu bar to access the Display Attributes control panel.
   • To change the display style, set the Style popup on the control panel.
   • To set the style preferences, click the Preferences... button in the Display Attributes control panel to open the Style Preferences control panel and set the corresponding parameters.

Measuring Distances, Angles, Torsion angles, etc.

Distances, angles, planes, torsions, and inversions for the atoms in a model can be measured and displayed in the model window or the text window.

1. Click Geometry/Measurements to access the Measurements control panel.
2. To measure the distances between atoms:
   • Click and then pick atom pairs (need not be bonded to each other) whose distances you want to measure.
   • Or, select any number of atoms and then double-click . The lengths of each bond existing between selected atoms are measured.
   The measured distances are indicated in the model window with dotted lines.
3. You can also display all measurements in the text window by clicking the List measurements button.
4. To remove all measurements from the display, click the Delete measurements button.
5. To temporarily hide the calculated measurements, check the Hide measurements check box.
6. Try measuring the angle involving any three atoms, the angle between any two planes, the torsion angle involving any four atoms, and the inversion or out-of-plane angle involving any four atoms by clicking , , , and , respectively.

You can calculate and display too-close contacts that may occur between atoms.

7. Click Geometry/Close Contacts to access the Close Contacts control panel:

   

8. Two criteria can be used for determining close contacts:
   • To determine if the distance between the atomic centers is less than a specified cutoff distance, choose DISTANCE and enter the Cut-off in angstroms in the control panel.
   • To determine if the distance between the atom centers is less than a(r1 + r2), where a is a specified ratio and r1 and r2 are the van der Waals radii of the two atoms, choose VDW RADIUS and enter the VDW Ratio (a).
9. You can exclude certain atom pairs from the close contact calculation, such as BONDED atoms or atoms in the same GROUP, FRAGMENT, or MODEL.
10. Click the CALCULATE close-contacts button to calculate and display close contacts. Once calculated, close contacts are continuously updated when fragments are moved, rotated, cleaned, etc.
11. Click the Delete all close-contacts button to remove the close contact calculation.

You can display a compound (a molecule or a complex), or single crystallographic unit cell, or more than one unit cell as a model. If a FDAT (Cambridge format) file is loaded into the Cerius² program, the contents of a single unit cell (containing more than one compounds) will be displayed by default. You can change the display range to a single compound or to more than one unit cell:

1. Find the CRYSTALL BUILDER card on the BUILDER 1 module from the deck of cards menu, and click Crystal Building on the card to access the Crystal Building control panel.
2. Click the UNBUILD CRYSTAL button on the control panel to display only one compound with all others removed.
3. To change the display range back to a single unit cell, click BUILD CRYSTAL button on the Crystal Building control panel.
4. To display more than one unit cell:
   • Click Visualization on the CRYSTALL BUILDER card to access the Crystal Visualization control panel.
   • Enter the number of cells in three dimension in the Crystal Cell Display Range box, then click the ENTER button.

• To display the models in stereo mode -- 3D view, click View/graphics/stereo and check Stereo in the popup Stereo control panel.
• If the hardware stereo accessory is available on your computer (currently available only on splatter, stereo3, and in room A400), check Crystaleyes in the Stereo control panel.
• Wear the special LCD glasses and turn it on by pushing the button on it. You will see the image in 3D. Pushing the button again will turn it off.
• If the stereo hardware is not available, check Stereo-pair in the Stereo control panel. You will see a "stereo pair" (two images side-by-side that look like 3D images if you cross your eyes or get a pair of stereo lenses; stereo pairs are often seen in publications).

• <F1>  =  Help
• <F2>  =  Full-screen toggle
• <F3>  =  Perspective
• <F4>   =  Stereo toggle
• <F5>   =  Stereo mode
• <F10>  =  Single/Double buffer

DON'T forget to log out of the SGI workstation (click on Desktop/Log Out in the toolchest, then confirm that you want to log out) when you are completely finished.