THE GRASP MANUAL
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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)
     Color Coding
     Surfaces
     Electrostatics
     Distance Calculations
     Maps
     Atoms
     Bonds
     Contours
     Colors
     Subsetting
     Simple Property Mathematics
     Objects
     Matrix Representations
     Stereo / Split Screen Operations

    
Basic operations:  Getting Started (pgs 18-21)
     Environment Variables
     Paths
     Data Files

    
The Control Keys: Selective Short Cuts (pgs 22-27)
     The Grasp A-Z.

    
The Command Line: Inquiring by property (pgs 28-38)
     Coloring Objects
     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:
     Atoms
     Surfaces
     Bonds
     Backbone Boxes
     Matrix Strands
    
    
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)
     General Improvements
     Specific Projects:
             Intelligent DelPhi
             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)