available on the SGI hardware

Installation

1) Getting into the system on Silicon Graphics

2) Books and Pages

3) Picture Motion

4) Picture Examination

• Book 1 VIEW.
• LABELS & TYPES:
• ZOOM:
• SCALEDOWN:
• CHIRALITY:
• FIND 1 LABEL:
• ORTHOG VIEWS:
• BEST VIEW:
• CIRCLES:
• CROSS 3D:

• Book 2. CHANGE-
• NEW TORSIONALS, ANGLES & BONDS :
• COLOUR:
• SIZES:
• NEW TITLE:
• FRAGMENT MODE:
• SPIN A BOND:
• RENUMBER MOLECULE:
• INVERT ATOM:
• INVERT MOLECULE:
• OPTIONS:

• Book 3. MEASURE & REPLANE-
• DISTANCE:
• BOND ANGS & TORS ANGS
• XY PLANE:
• XZ & YZ PLANES:
• HEIGHT ABOVE PLANE:
• CENTRE OF MASS/CHARGE:
• CENTROID:
• NORMAL TO PLANE:

• Book 4. HIDE & SHOW-
• Book 5. ADD & REMOVE -
• ADD & REMOVE Hydrogens:
• ADD & REMOVE XEDs:
• REMOVE FIELDS:
• REMOVE ALL STRUCTURE:
• REMOVE ALL DUMMIES:
• REMOVE A FRAGMENT:
• REMOVE 1 MOLECULE:
• ADD & REMOVE BOND:
• REMOVE ATOMS:

• Book 6. PROCEDURES -
• FIT MOLECULES:
• CONFORMATION HUNTER:
• DOCK 2 MOLECULES:
• SEQUENTIAL DOCK:
• SPIN BARRIER:
• TORSIONAL DYNAMICS:
• CALCULATE A FIELD:
• OVERLAY 2 FIELDS:
• MOPAC- RUN & LOOK:

• Book 7. INPUT & OUTPUT-
• AT THE FILENAME PROMPT
• READ CCDC FILES:
• R/W DIFFERENT FORMATS:
• SAVE CURRENT STRUCTURE:
• WRITE:
• READ (CLEAR SCREEN)
• For a single-molecule file:
• For a multi-file:
• READ (ADD A .DAT):
• Book 8. No Cover -
• DRAW:
• Building a Structure from scratch:
• DRAW Book 5:
• POINT TOLERANCE:
• PEPTIDE BUILD:
• DRAW Book 6:
• SCALEDOWN:
• ZOOM:
• REMOVE 1 ATOM:
• REMOVE 1 BOND:
• JOIN:
• DRAW Book 7:
• UNDO:
• GET LAST STRUCTURE:
• DRAW Book 8:
• RESET:
• TO VIEW:
• MINIMISE/CHARGE:
• HARD COPY:
• UNDO:
• RESET:
• FINISH:

5) The BATCH Submission Procedure.

6) ASTRAL. Viewing Multi-Files

• Colour Code:
• Picture Movement:
• Picture Manipulation:
• Menu Items:
• Increment/Decrement.
• Animation.
• Rescale.
• Display a Chosen Energy Range.
• Display a Chosen Number Range.
• Store.
• Turn on All Objects.
• Toggle Atom/Energy Colours.
• Return to Top Window.
• The ESC key.
• Function Keys in ASTRAL:
• F1:
• F2:
• F3:
• F4:

7) Trouble Shooting

8) Appendices

• APPENDIX 1 A DRAWING EXERCISE
• APPENDIX 2 XED/COSMIC ATOM TYPES
• APPENDIX 3 XEDs - THEIR MEANING & USE
• APPENDIX 4 XED/COSMIC MINIMISATION
• a) The Molecular Mechanics:
• b) The 'Single Shot' Minimiser:
• c) The Conformation Hunter:
• APPENDIX 5 FILE FORMATS
• ACKNOWLEDGEMENTS.
• INSTALLATION, NOTES AND LATE INFORMATION.