the goodman group
university of cambridge  


   sybyl notes

The Silicon Graphics Teaching Laboratory
has been replaced by the
Chemi cal Information Laboratory
and this information is for historical interest only

Sybyl Notes

Mouse | Top Menu | Left Column | Display Areas | Function Keys | Scripts

Sybyl is a general molecular modelling program written by Tripos. We are grateful to GlaxoWellcome for donating a licence to the Department of Chemistry.

Documentation (only available from SGTL machines)

To run the program, type sybyl.

Sybyl screen


Mouse Buttons

The mouse buttons should be used individually or in pairs for the illustrated effects:

With the exception of scale, these operations can be performed on one or all four (Global) of the display areas by swapping between them in the normal way.


The Top Menu

The top bar contains a series of pull-down menus which contain all of the building, viewing, and calculation routines in Sybyl. Beware that some parts of the program require a separate licence to run. If you require a routine that is not currently licenced to the Chemistry Department, please contact Jonathan Goodman.

For a brief summary what each menu contains, click on the appropriate key below.


Graphics Tools

The left column contains a number of gadgets that are extremely useful when manipulating and viewing molecules. These are briefly summarized below.

Advert for Tripos Also a variety of telephone numbers by which to contact Tripos, which are useful for those who pay for telephone support (The SGTL does not).
Display Areas Choose whether to manipulate all display areas (G for Global) or just one of D1, D2, D3, D4.
Screen Options Controls how molecules are displayed (ball and stick, spacefilled), the screen format (quartered, full) and various stereo modes.
Display Options This toggles molecules and backgrounds in the 4 display areas on and off. The atom labels expecially useful.
Reset This resets rotations and translations in the display areas. Unless a VIEW>FREEZE VIEW is issued, molecules can always be reset.
Rotate bonds Allows you to twist torsion angles. It is limited to 6 bonds per gadget, but allows unlimited gadgets.
Z-Clip Controls Z-clipping. Pronounced "Zee-clipping" by the Americans.
Depth Cueing Controls depth cue. Default is 100% fading.
Windows Brings Sybyl windows to the front of the screen
Stereo Controls spacing between molecules when in stereo mode.
Physical dial box This is not useful unless you have a physical dial box.
Virtual Dial Box Acts much like the Alchemy rotation/translation controls.
Rate mode Excellent for hands-off molecule rotation. Good to impress management.

Top Menu : File

OPTION Description
Read Reads molecules in various formats. Sybyl standard format is .mol2
Save As Writes molecules and suchlike. Both .mol2 and .pdb formats
Database A file containing multiple molecules. Good for organizing projects.
Molecular spreadsheet Sybyl's spreadsheet - can accept molecules in cells
Log commands Saves commands as a macro
Take commands... Reads a macro ("take" file in Sybylspeak)
Log session Records commands during a session
System Window Allows the user to issue UNIX commands. Type "exit" to return to Sybyl.
Plot Postscript or HPGL
Exit Vaya con dios

Top Menu : Build/Edit

Undo Undo last action. All is not lost...
Zap molecule Deletes one or more molecules
Get fragment Gets molecular fragment from Sybyl's library
Sketch molecule Sybyl's sketching tool. The fastest way to build a molecule
CONCORD/SMILES Converts from SMILES to 3-D. Requires a CONCORD licence.
Clean-Up Performs a torsional hunt or rough dynamics.
Name molecule Most molecules answer to "Fred".
Center... Centres the molecule on one or more atoms.
Copy... Copies a molecule from one molecule area to another
Merge... Combines two molecules into one molecule area
Extract Copies a part of a molecule into another molecule area
Aggregates... Fixes part of a molecule for purposes of minimisation.
Constraints... Applies bond stretch, angle, and torsion constraints.
Add Adds atoms, bonds, etc.
Define Defines sets, centroids, normals and planes
Delete Deletes atoms, bonds, etc.
Modify Modifies atoms, bonds, atom types etc. (Necessary for good force field results)
Other Tools Chirality and fusion tools
Crystals Crystal structure viewing options.
Solvent Solvation options.

Top Menu : View

Color Colours molecules, atoms, bonds or labels.
Display Atoms Selectively displays atoms or monomers...
Undisplay Atoms ...and then hides them.
Label Selectively labels atoms, bonds, or substructures, by ID or type...
Unlabel ...and then hides the labels.
Center of Rotation Allows the user to change the centre of rotation.
Freeze view Freezes molecules in current orientation/location. Necessary after docking.
Delete all backgrounds Deletes all backgrounds
Background Reads, writes, lists, and changes the colours of backgrounds
Annotation Puts labels, arrows and titles onto screen.
Rendering Options... Controls the Display Options gadget in left hand column.
Mixed Rendering... Creates a spacefilled, ball-and-stick, or stick version of the molecule.
Dot surfaced Creates a vdW or Connoly dot surface.
Contour surfaces Creates volume or isopotential surfaces. These are large files.
Shaded surfaces... Apply shading to a previously calculated surface.
Display H-Bonds Creates a static or dynamic display of hydrogen bonds.
Monitor Dynamically updates distances and hydrogen bonds during manipulation.
Constraints View constraints added previously.
Ruler Add a ruler to the display window
2D Viewer Converts molecule to 2-D structure
Backdrop Changes backdrop style

Top Menu : Compute

Minimize... Minimizes using the Tripos or Kollman (AMBER) force fields.
Minimize subset Minimizes only a portion of the molecule.
Dock Perform a docking simultion.
Energy Computes the energy of a given molecule.
Multifit Fits two molecules together with energy minimisation.
Superimpose An alternate method of fitting. Can also fit on electrostatic fields.
Charges Calculates atom-centred charges using a variety of algorithms.
Dipole... Calculates the magnitude and direction of a molecular dipole.
Force field parameters Add,view, or modify parameters.
Multiple DG Embedding... Specifies bounds for distance geometry simulations.
Distance Geometry Uses distance geometry to do a conformational search or docking.
Molecular mechanics Minimisation using the MM2 force field.
Dyamics Menus to set up molecular dynamics and simulated annealing simulations.
BOSS Monte Carlo simulation or free energy perturbation.
Search Torsional searches : grid, random, or systematic searches.
AutoCOMFA Interface to COMFA routines. This requires a COMFA licence.
Interfaces to MOPAC, ZINDO, EHMO, Gaussian, CCDC, Medchem, and DGEOM (not all available).
Netbatch Distributes jobs among a group of computers.

Top Menu : Analyze

Measure Measures distances, angles, torsions and suchlike.
Match Overlays molecules. Atom matching is in order chosen.
Fit atoms Also overlays molecules. Requires pairwise picking of atoms.
Superimpose... Superimposes two molecules.
Distance Geometry Analysis of DGEOM results.
Molecular Mechanics Analysis of MM2 minimisations.
Dynamics Analysis of MD simulations.
BOSS Analysis of BOSS simulations.
Search Analysis of conformational searches.
Interfaces Analysis of other calculations.

Top Menu : Options

Set Changes defaults. Try SET BOND 3 to improve graphics on some terminals.
Tailor Changes defaults for many calculations and routines. Check the menu for details.
QSAR Sets up a molecular spreadsheet with QSAR options.
Biopolymer Opens a peptide building and analysis menu. This appears on the Top Menu.
Info Lists molecular information.
List Lists other useful information.

Top Menu : Biopolymer (Choose from "Options" Menu)

Build Builds proteins, nucleic acids or carbohydrates.
Brookhaven File Reads or writes .pdb format files.
PIR File Reads or writes PIR format protein sequence files
Add Hydrogens... Adds hydrogens to a protein structure
Add Sidechains... Builds sidechains onto a protein backbone trace
Load charges Loads atom-centred charges from a sidechain library
Conformation Tools to measure and set protein conformation
Modify Tools to delete, insert and mutate protein residues
Fit Monomers Fits two protein chains
Find and Fit Fixed Regions... Automatically fits similar regions. Useful for homology modelling.
Analyze Protein (ProTable) A useful protein analysis tool. Requires a separate licence.
Display Ribbon and tube tracings of protein backbone.
List sequence... Lists a protein sequence.
Align sequences... Sequence alignment tool.
Predict secondary... Predicts the secondary structure of a protein sequence.
Search protein database Searches a proprietary version of the Brookhaven database
Protein Loops... Homology modelling tool for protein loops.
Monomer dictionary.. Provides access to the dictionary of monomers.

Display Areas

Sybyl has four display areas: D1, D2, D3, D4. The default setting is G (global), and this means that rotations, translations, etc will apply to all the molecules. By clicking the Display Area button, you can choose a particular display area to manipulate. The Display areas may be superimposed, or quartered around the screen in the order shown in this figure:

To control whether or not to have quartering, use the Screen Options button.


Molecular Areas

Whenever you read a molecule from a file, or start drawing on the screen, you will be asked which molecular area you want to use. The name of each area is M#, where # is a number. The work area name associated with a molecule does not change during a session. If you are working with several molecules, you can distinguish them by their molecular area name.

The Molecule Areas are associated with Display Areas in the following manner:

  • D1 : M1, M5, M9, M13 ...
  • D2 : M2, M6, M10, M14 ...
  • D3 : M3, M7, M11, M15 ...
  • D4 : M4, M8, M12, M16 ...

Backgrounds and Backdrops

Background displays are graphical information other than the molecule itself. These include the various types of surfaces and other images that Sybyl can create. These images are attached to a particular display area and respond to rotations, translations, etc just like any molecule in the same display area.

A Backdrop is the colour or image behind the molecules and backgrounds. By default, this is black, but can be changed to other colours or patterns using the Backdrop option of the View menu.


Function Keys

F1 Hides the text window. Press F1 again to toggle back.

F5 Toggles between photo and normal display modes.

F6 Toggles toolbox icons on and off.

F7 Toggles hardware stereo on and off.

F8 Raises or lowers graphics window, when hardware stereo is active

F9 Toggle between D1 and G

F10 Toggle between D2 and G

F11 Toggle between D3 and G

F12 Toggle between D4 and G

Cursor left
Rotate +90 degrees around the y-axis

Cursor right
Rotate -90 degrees around the y-axis

Cursor up
Rotate +90 degrees around the x-axis

Cursor down
Rotate -90 degrees around the x-axis

Ctrl
Hold down Ctrl in combination with a left mouse click to select a molecule or background for object transformation.

Scripts

Sybyl has a powerful scripting language. An archive of Sybyl scripts is available from the Rennselear Polytechnic Institute.

Information on Graphics, including how to change the colour of the screen (backdrop) is available from Tripos.




© Goodman Group, 2005-2017; privacy; last updated October 19, 2017

department of chemistry University of Cambridge