|THE GRASP MANUAL
GRASP: Graphical Representation and Analysis of Surface Properties
Introduction: Why Grasp became what it is (pgs 1-4)
Features: What Grasp can do and what it cannot do (pgs 5-17)
Simple Property Mathematics
Stereo / Split Screen Operations
Basic operations: Getting Started (pgs 18-21)
The Control Keys: Selective Short Cuts (pgs 22-27)
The Grasp A-Z.
The Command Line: Inquiring by property (pgs 28-38)
Mapping Atoms Colors to the Surface
Undo and Restore Coloring
Precise Translations and Rotations
Listing Atom Properties
Changing Atom and Surface Information Fields for Mouse Picking
Altering Radii and Charges
Specific Grasp Syntax for Negation, Concatenation and Projection
General Grasp Subsetting Syntax:
The Menus: Doing everything else (pgs 39-67)
Display (or not) Structures in a Particular Form.
Build and/or Calculate Structures and Structural Properties.
Mouse Functions, (and how to alter them).
Read and Write Grasp data files.
Formal Subset Operations.
Other Programs, i.e. Superimpose.
Setting Internal Parameters.
Miscellaneous, Help and Quit.
Worked Examples (pgs 68-73)
Getting a molecular surface color coded by electrostatic potential.
Displaying surface potential and surface curvature side by side.
Surfacing two interacting parts of a molecule and selecting an interface.
Calculate the occluded accessible surface area between these parts.
Reading in atomic B-values from a PDB file, displaying them on the surface.
Calculating and displaying the effective dielectric from a single charge site.
Calculating average surface areas per hydrophobic and hydrophilic residue.
Finding and displaying all residues within 3 Angstroms of an active site.
Finding the common volume between two superimposed molecules.
Forming a six helix bundle from a single helix and surfacing the result.
Future Developments (pgs 74-82)
Secondary Structure Display
Docking with Realistic Energies
Appendices A, B and C (pgs 83-89)
Appendix A: File Formats
Appendix B: .init_grasp commands
Appendix C: Grasp data files
Addenda (pgs 90-92)
References (pg 93)