CZ3253 Practical 1: An Introduction to Sybyl
 

SYBYL 7.0 Basics

• Starting Sybyl
  • /share/tripos/trigo/sybyl7.0

   

• Menubar
  • SYBYL's menubar is similar to that of a PC application's menubar. The presence of an active (black font) SYBYL menubar indicates that the program is waiting for your menu selection.
  • A menu item can be a simple command or a check box; it can also lead to a submenu or a dialog. Additional categories may be available if you have licensed special modules.
  • By default, all options are shown in the menus. Any options for which you do not have a license are greyed out (these most likely will occur in the Tools menu).

   

• Toolbox Icons
  • The SYBYL tools used to interact with the graphics are represented by icons along the left edge of the SYBYL screen.
  • To activate an icon, place the pointer on it and press the left mouse button. In cases where a dialog is displayed, you can close the dialog by pressing the Q button.
  • From the top to bottom, the graphics icons are:
    Support Information, Mouse Focus, Display Options, Display Area Options, General Structure Display, Graphic Attributes, Reset, Rotatable Bonds, Z-Clipping, Depth Cue, Restack, Stereo Adjustment, Physical Dial Box, Virtual Dial Box, Extents and Rate Mode.
     
• Textport Window
  • The textport window enables you to enter any command, including HELP. Review the Tripos Bookshelf for a complete listing of all SYBYL commands available. After entering a command, the prompt is again printed on the terminal.
  • Note: When running SYBYL, both menu selections and command line entry are available simultaneously.

   

• Help
  • The Tripos Bookshelf is SYBYL's online help tool. This interactive documentation enables you to view Tripos documentation online. It is context sensitive and is a valuable tool to help you learn more about SYBYL.
  • The Tripos Bookshelf contains:
    Index, Connection to Tripos web site, Full color pictures, FAQs, Search functionality, Citations, Articles, Work flow charts, PDF library.
     
• Mouse Buttons
  • The left button is used to select SYBYL menu items/objects (by picking atoms), to open/close graphics icons, and to select items in the dialogs.
  • Pressing mouse button combinations and moving the mouse cause various motions of objects in the "active" display area, below is a summary table:

Mouse button	Function
left	selection
mid + right	scale
right	X-Y rotation
left + right	Z rotation
mid	X-Y translation

   

Working with Molecules

• Load Molecules from the Fragment Database
  • Build/Edit >>> Get Fragment
  • Example:
    • Load 1,3-DIOXANE into SYBYL.
      • Build/Edit >>> Get Fragment.
      • Select 1,3-DIOXANE.
      • Press OK.
      • The molecule loads into SYBYL's display area 1, also known as D1. Its default location is in molecule area 1, also known as M1.
        • A molecule area is a region of memory that holds a particular molecule. Molecule areas do not have a defined number (the number depends on the computer's memory). You can place hundreds (if not thousands) of molecule areas in a display area on a standard workstation.
        • A display area is where your molecule is going to be displayed on the screen. SYBYL has four unique display areas: D1, D2, D3, and D4.
        • Note that molecule areas have rules:
          
          M1 is always in display area D1.
          M2 is always in display area D2.
          M3 is always in display area D3.
          M4 is always in display area D4.
          
          If additional molecule areas are used, they simply recycle through the display areas:
          
          M5 is always in display area D1.
          M6 is always in display area D2.
          M7 is always in display area D3.
          M8 is always in display area D4.
    • Change the characteristics of your loaded molecule.
      • Press .
        The Display Options dialog is displayed. This dialog enables you to modify the various look of your display area and molecules.
      • In the Display Options dialog, select Sticks.
        The lines making up your molecule become thicker and the color codes are more defined. From now on, if you load any molecule in SYBYL, it will load in Sticks mode.
      • Press Q to close the Display Options dialog.
    • Load another molecule into SYBYL.
      • Build/Edit >>> Get Fragment.
      • Select 1,2,4-Trioxolane.
      • Press OK.
      • M1 is already being used by 1,3-dioxane. However, the other molecule areas (M2 - M10) are currently empty. You must choose which molecule area should house the newly loaded molecule.
      • In the Molecule Area dialog, select M2:<empty>.
      • Press OK.
      • You have now placed two molecules within SYBYL (1,3-Dioxane and 1,2,4-Trioxolane). The two molecules reside in two unique molecule areas (M1 and M2).
• Read/Write Files of Molecules
  • Read in Structure from File via the Menubar
    • To open a file for reading, select File >>> Read.
    • The Read File dialog uses the filename as the default for the molecule name when reading a single file. If any form of molecule name is present in the input file, that name is used instead.
  • Write out Structure from File via the Menubar
    • Select File >>> Save As.
    • Specify Format.
    • Multiple structures can be selected from the list and saved to a MOL file, MOL2 file, SD File, or SLN file. Use the Select All, Invert, and Clear buttons to manipulate the selections in the molecule list.
      • MOL2 files are ASCII files containing all information necessary to reconstruct the molecule. The format is based upon the convention of a keyword for each type of data needed to reconstruct the molecule, followed by a group of records.
      • A MOL file does not preserve the complete information available with molecules in SYBYL 6.x and above. It is provided for compatibility with existing user programs. Data written to a MOL file include atoms and bond information, rotatable bond definitions and plane equations. To preserve the complete molecular description, use the MOL2 file format.
• Rotate the Molecules
  • Use the Mouse Focus Option dialog to differentiate between the two molecules that were previously displayed:
    • The display area is set to Global by default when you start a SYBYL session. All images on the screen -- molecules and backgrounds -- are affected simultaneously by rotations and translations.
    • Rotate the molecules by pressing the right mouse button and moving your mouse in any direction.
    • Notice that both molecules move. This is because your current molecule setting is on Global (global).
  • Move 1,3-DIOXANE to the upper right corner:
    • Press the button.
    • Select D1 in the Mouse Focus Options dialog.
      By selecting D1, you are telling SYBYL to focus in on 1,3-DIOXANE.
    • Press the middle mouse button and move 1,3-DIOXANE to the upper right corner of SYBYL.
  • Move 1,2,4-TRIOXOLANE to the upper left corner:
    • Unselect D1 and select D2 in the Mouse Focus Options dialog.
      By deselecting D1 and selecting D2, you are telling SYBYL to focus in on 1,2,4-TRIOXOLANE.
    • Press the middle mouse button and move 1,2,4-TRIOXOLANE to the upper left corner of SYBYL.
• Clear the Screen
  • Build/Edit >>> Zap (Delete) Molecule
  • ZAP deletes molecules and their associated data structures from program memory. It clears the molecule area. All associated display structures (e.g., dots, ribbons, ...) are removed from the graphics screen as well.