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Concept Index

1

  • 1-4 Non-bonded Scaling

    2

  • 2DPLOT Command
  • 2DPlot Command

    3

  • 3TER residues

    5

  • 5TER residues

    a

  • Ab initio Calculations
  • Abbreviations
  • Abbreviations of Residues
  • ABNR Minimization
  • Acceptor (HB) Generation
  • Acceptors of Hydrogen Bonds in the RTF
  • Accessible Surface
  • Accessible Surface Coloring
  • Accessible Surface Drawing
  • ADD Command Syntax
  • Adding Statistics to a Table
  • Adding Water Molecules
  • Adopted Basis Newton-Raphson Minimization
  • AKMA
  • All Hydrogen Topology Files
  • ALLCHP
  • ALLCSTK
  • ALLDT
  • ALLHP
  • Allocation of Dynamic Memory
  • ALLSTK
  • Alpha Carbon Plots
  • Alpha-carbon Displays
  • AMBER 94 parameters
  • AMBER parameters
  • AMBER Potential
  • AMBER94RTF
  • AMBERUNIRTF
  • Amide Torsion Energy (AMBER94)
  • Amino Acid One Letter Code
  • Analysis Data I/O
  • Analysis END Command
  • Analysis of Conformations
  • Analysis of Poisson-Boltzmann Electrostatics
  • Analysis Set Command
  • Analysis Twist Command
  • Analysis Variables
  • AND
  • Angle Energies
  • Angle Generation
  • Angle Properties
  • Angle Specifications in the RTF
  • Angles
  • Annealing
  • ANSI C Function Prototypes
  • Areas, Atomic Surface
  • ASGNDT
  • Atom Attribution of Poisson-Boltzmann Energy
  • Atom Labeling
  • Atom Manipulations for Sphere Drawing
  • Atom Masses
  • Atom Matching
  • Atom Ordering
  • Atom Patch Charges
  • Atom Selection
  • Atom Selection in Sphere Drawing
  • Atom Selection Operators
  • Atom Specifications in the RTF
  • Atom Static Properties
  • Atom Type Code Patterns
  • Atomic Attribution of PBE Energy
  • Atomic Charge
  • Atomic Charges
  • Atomic Constraints
  • Atomic Polarizability
  • Atomic Radii
  • Atomic Surface Areas
  • Atomic Volumes
  • Atoms in Sidechain Topologies
  • Attributes of Residues
  • Auto-Correlation Functions
  • autodoc
  • Automatic Generation
  • Automatic Scaling for Sphere Drawing
  • Average Coordinate Writing
  • Averaging Two Coordinates

    b

  • Backbone Construction
  • Backbone Construction Maps
  • Backbone Construction Order
  • Backbone Degree of Freedom
  • Backbone Energy Maps
  • Backbone Twist
  • Background Color for Spheres
  • Base Array
  • Binding Energy
  • Binding Energy Calculations
  • Bond Angle Energies
  • Bond Angle Specifications in the RTF
  • Bond Angles
  • Bond Energies
  • Bond Lengths
  • Bond Properties
  • Bond Specifications in the RTF
  • Boolean variables
  • Boundary of Grid
  • Boundary, Electrostatic
  • Brookhaven Protein Data Bank
  • Brookhaven to Congen Conversion
  • BUILD Command Syntax
  • BUILD information
  • Builder Rule Generation
  • Building CONGEN
  • Building from torsion angles
  • Building Tables

    c

  • C
  • C Function Prototypes
  • Carbon Monoxide Patching
  • Cases of File Names
  • Cavity Energy
  • CG directory
  • CG Files
  • cg_new_node_q
  • cg_work_q
  • CGBIN directory
  • CGD directory
  • CGDATA directory
  • `cgdefs'
  • CGLIB directory
  • CGP directory
  • CGPLATFORM
  • `cgprofile'
  • CGPS directory
  • CGROOT Directory
  • CGS directory
  • CGT directory
  • CGTD directory
  • Chain Closure
  • Charge Calculation
  • Charge on Atoms
  • Charges
  • Charges, Atomic
  • Charges, Patch Atoms
  • Checkpoint File
  • Checkpointing Conformational Searches
  • Chemical Type Codes
  • Chiral Atoms (AMBER94)
  • Cis-Trans Peptide Isomerization
  • Classes of Tables
  • Cleaning of Tables
  • Clearing the Sphere List
  • Close Contact Searches
  • Closing a File
  • CLSCHN
  • Clumps in Sidechain Topologies
  • CO Parameters
  • Codes Command
  • Coding Rules for I/O
  • Coding Standards
  • Collection of Table Data
  • Color Resetting for Sphere Drawings
  • Colors
  • Colors for Accessible Surface
  • Colors of Atoms for Sphere Drawing
  • Columnar Table Printing
  • Command Abbreviations
  • Command files
  • Comments
  • Common Blocks
  • Common Blocks for Data Structures
  • COMPARE Command Syntax
  • Comparing Coordinates
  • Comparison by Homology
  • Comparison Coordinate Set
  • Comparison Coordinate Writing
  • Comparison Coordinates
  • Comparison coordinates
  • Comparison Data Structures
  • Comparison Messages
  • Comparison of Conformations
  • Comparison Tables
  • Comparisons
  • Comparisons of Conformations
  • Compiler Flags
  • `config.h'
  • Conformation File Operations
  • Conformation File Reading
  • Conformation Files
  • Conformational Search
  • Conformational Search Examples
  • Conformational Search I/O
  • Conformational Search Limits
  • Conformational Search Method
  • Conformational Search Related Commands
  • Conformational Search Strategy
  • Conformational Search, Reducing Output
  • Conformational Search, Reducing Outputs
  • Conformations File
  • CONGEN Command Syntax
  • Congen introduction
  • CONGEN Modifications
  • CONGEN Testing
  • Conjugate Gradient Minimization
  • Conserved Residues
  • Constant Dielectric
  • Constants of Geometry
  • Constants, Numeric
  • Constraint Command
  • Constraint File for NMR
  • Constraint Reading
  • Constraints
  • Construction of Backbone Energy Maps
  • Construction of Hydrogen Positions
  • Construction of Prolines
  • Construction of Small Molecules
  • Construction of Tables
  • Construction of Unknown Positions
  • Contact Surface
  • Continuations lines
  • Control
  • Conversion of Brookhaven Formats
  • Conversion of peer files
  • Conversion to SGI RGB Format
  • Conversion, IMP to PBE
  • Coordinate Averaging
  • Coordinate Comparison
  • Coordinate Constraints
  • Coordinate Conversion, Brookhaven
  • Coordinate Copying
  • Coordinate Differences
  • Coordinate Displacement Arrays
  • Coordinate file format
  • Coordinate Fitting
  • Coordinate Initialization
  • Coordinate Manipulations
  • Coordinate Matching
  • Coordinate Orientation
  • Coordinate Properties
  • Coordinate reading
  • Coordinate Rotation
  • Coordinate Scaling
  • Coordinate Swapping
  • Coordinate Transform Inversion
  • Coordinate Transforms
  • Coordinate Translation
  • Coordinates
  • Coordinates after Conformational Search
  • Copying Coordinates
  • Copying RTF Residues
  • Copying Sidechain Topology Residues
  • Copyright Notices
  • Core Dumps
  • Core size
  • Correlation Function Calculation
  • Correlation Function Manipulations
  • Correlation Functions
  • CPK Models
  • CPP
  • CPU Time for BUILD Command
  • CPU Time Limits
  • CPU Times
  • Crystal Parameters
  • Crystallographic Images
  • CSTACK
  • CSTKSIZ
  • CTER residues
  • Cut Data from a File
  • cutoffs, hydrogen bond
  • Cutting a Sphere Drawing
  • Cyclic Peptides

    d

  • D Amino Acids
  • Dashed Lines
  • Data Deletion in Tables
  • Data Manipulation Commands
  • Data Structures
  • Data Structures for Comparisons
  • Data Structures for Non-bonded Interactions
  • Data Structures on the Heap
  • Data Structures, Poisson-Boltzmann
  • data-structure
  • DBG_ALLSTK
  • DCL commands
  • DEANZA
  • Debugging
  • Debugging a Conformational Search
  • Debye-Huckel Parameter
  • Deepening Evaluation Strategy
  • Define Colors for Sphere Drawing
  • Degree of Freedom
  • Deleting Data from Tables
  • Deletion from Difference Tables
  • Deletions in a Sequence
  • delimiter
  • Delimiter Usage
  • Delimiters
  • Depth First Search
  • Derivatives of the Energy
  • DEVAL Search Strategy
  • Device Setting for Sphere Command
  • DIE subroutine
  • Dielectric Averaging
  • Dielectric Constant
  • Dielectric Smoothing
  • Difference in Coordinates
  • Difference Table Deletion
  • Difference Tables
  • Differences in Coordinates
  • Diffuse Coefficient of Lighting
  • Dihedral Angle Energy
  • Dihedral Angle Properties
  • Dihedral Angle Specifications in the RTF
  • Dihedral angles, building molecules from
  • Dihedral Constraints
  • Dimensions of Sphere Drawing
  • Dipole Electrostatic Approximation
  • Dipole, Induced
  • Directed Conformational Search Example
  • Directed Searching
  • Directory Names
  • Display Lighting Parameters
  • Display Sphere Drawing Parameters
  • Displaying Sphere Drawings
  • Distance Computation
  • Disulfides
  • Division by Zero
  • DNA Parameter Files
  • DNA Parameters
  • DNA Sequences
  • DNA Topology Files
  • Donor (HB) Generation
  • Donors for Hydrogen Bonds
  • Donors of Hydrogen Bonds in the RTF
  • Double Precision
  • Drawing Structures
  • DT_NUMERIC
  • Dummy non-bonded Interactions
  • DUPLDT
  • Dynamic Storage Allocation
  • Dynamics
  • Dynamics trajectories, reading
  • Dynamics Trajectory Reorientation

    e

  • Editing Hydrogen Bonds
  • Editing the PSF
  • Editing topology files
  • Effective Number of Electrons
  • Electrons, Effective Number
  • Electrostatic Boundary
  • Electrostatic Charges
  • Electrostatic Interactions
  • Electrostatic Potential
  • Electrostatic Properties
  • Electrostatics
  • emap
  • emappro
  • EMAX variables
  • END Command, Analysis
  • Ending Execution
  • Ending Sphere Drawing
  • Energies with symmetric images.
  • Energy Calculation Prerequisites
  • Energy Calculations
  • Energy Derivatives
  • Energy Directed Conformational Search Example
  • Energy Evaluation Codes
  • Energy Maps
  • Energy Properties
  • Energy Weights
  • Energy, solvation
  • Ensemble Averaging
  • Environment Variables
  • Equilibrium Geometries
  • Error Handling
  • EVAL Search Strategy
  • Evaluation of Conformations
  • Evaluation Strategy
  • Evans and Sutherland Display
  • Example of Energy Directed Search
  • Example of Five Residue Search
  • Example of PBE in Conformational Search
  • Example of Sidechain Reconstruction
  • Examples
  • Examples of Conformational Search
  • Examples of Poisson-Boltzmann Usage
  • Examples of Sphere Drawing
  • Examples, IMP Usage
  • Exceptions, Floating Point
  • EXCH
  • EXCL
  • Exclusions from Non-bonded Interactions
  • Execution Times
  • Exiting from Sphere
  • Expanded Nodes
  • Explicit Hydrogen Topology Files
  • Extended Atom Topology Files
  • Extended Electrostatics
  • Extract Data from a File
  • Extracting Conformations

    f

  • F77 macros
  • FCPP
  • File Closing
  • File Name Cases
  • File Opening
  • File Rewinding
  • File Size Limit
  • Files Available
  • Files for Images
  • Filtering Conformers
  • Finite Difference Methods
  • Fitting of Coordinates
  • Fixed Atom Constraints
  • Fixed Atom Construction
  • Fixed Atoms
  • Fixing Bond Lengths or Angles
  • Fixing Bonds and Angles
  • fixmake
  • FLECS
  • Floating Point Exceptions
  • Flushing Output Buffers
  • Force Constant
  • Force Constants
  • Force Drawing
  • Force Properties
  • Format of coordinate files
  • Fortran
  • Fortran C Preprocessor
  • Fortran Pointers
  • Fractional Coordinates
  • FRECHP
  • FRECSTK
  • FREEDT
  • FREHP
  • FRESTK
  • FSIZEOF

    g

  • Gamma Correction
  • Gaussian Program
  • GEAR
  • Gear Method
  • Generate Command
  • Generating a Structure
  • Generation of angles, torsions, etc.
  • Generation of Non-bonded Exclusions
  • Generation of Non-bonded Interactions
  • Generation of Residue Components
  • Generation of Structures
  • Geometric Constants
  • GEPOL Calculation
  • GETE
  • Global Options for Conformational Search
  • Glossary
  • Glossiness for Spheres
  • GNU Emacs
  • Go and Scheraga procedure
  • Go and Scheraga Procedure
  • Graphics
  • GRID
  • Grid Boundary
  • Grid Charging
  • Grid Dimension
  • GROUP Commmand

    h

  • Harmonic Atom Constraints
  • Harmonic Constraints
  • HDR
  • Heap Management
  • Heap Storage
  • HEME group patching
  • Heme Parameters
  • HISTO Command
  • Histograms
  • Homologies
  • Homology of Sequence
  • Hydrogen Bond (HBOND) List
  • Hydrogen Bond Acceptors in the RTF
  • Hydrogen Bond Analysis
  • Hydrogen Bond Donor/Acceptor Generation
  • Hydrogen Bond Donors in the RTF
  • Hydrogen Bond Editing
  • Hydrogen Bond Energy
  • Hydrogen Bond Energy (AMBER94)
  • Hydrogen Bond Generation
  • Hydrogen Bond Parameters
  • Hydrogen Bond Properties
  • Hydrogen Bond Reading
  • Hydrogen Bonds
  • Hydrogen Position Construction

    i

  • I/O
  • I/O Coding Rules
  • I/O for Conformational Search
  • I/O for the Poisson-Boltzmann Equation
  • I/O in Analysis
  • I/O of Atomic Constraints
  • I/O with Tables
  • ICNTRL
  • Identifier Deletion in Tables
  • Image (Spheres)
  • Image Files Reading
  • Image Format
  • Image Sizing for Sphere Command
  • Images
  • Images, hydrogen bonds
  • IMOVE array
  • IMP usage examples
  • Implementation of CONGEN
  • Implementation of Non-bonded Interactions
  • Improper Dihedrals
  • Improper Torsion Angle Properties
  • Improper Torsion Energies
  • Improper Torsion Energy
  • Improper Torsions in the RTF
  • Index Common Block
  • Induced Dipoles
  • Induced Multipoles
  • Inducible Multipole Solvation Modeling
  • Inexact Errors
  • INISTK
  • INITDT
  • INITHP
  • Initialization of Coordinates
  • Initialization of Sphere Drawing
  • Initialization of Sphere List
  • Input
  • Input File
  • Input Rotation Matrix
  • Insertions in a Sequence
  • Installation of CONGEN on UNIX
  • Installation of CONGEN on VMS
  • Interactive Display
  • Interfacing to CONGEN
  • Interlanguage Interface
  • Internal Coordinate Command Syntax
  • Internal Coordinate Concepts
  • Internal Coordinate File Structure
  • Internal Coordinate Generation
  • Internal Coordinate Properties
  • Internal Coordinates
  • Internal Coordinates (IC)
  • Internal Coordinates in the RTF
  • Invalid Floating Point Exceptions
  • Inversion of Coordinate Transforms
  • Ionic Strength
  • Iris 4D Display
  • Iteration control (IMP Command)
  • IUPAC
  • IUPAC Name Translations

    j

  • J Coupling Constraints
  • J-coupling Constraints
  • Joined J coupling constraints
  • Joined J Coupling Constraints

    k

  • Karplus Equation
  • Keyboard Usage in Peer
  • keyword
  • Konnert Hendrickson coordinate file format
  • Konnert-Hendrickson Format

    l

  • Labeling a Plot
  • Language Interface
  • Least Squares Rotation and Translation
  • Length Array
  • Lighting of Spheres
  • Lighting Range for Spheres
  • Lighting Spheres
  • Lighting Vector for Spheres
  • Limits of Arrays
  • Line Drawings
  • Line Width
  • Linearized Poisson-Boltzmann equation
  • Linkage Atom Naming
  • Local Storage
  • Log file
  • Logical Names
  • Lower Case File Names
  • LSTCUSD
  • LSTUSD

    m

  • makefile.gen
  • Making a Sphere Drawing
  • Making CONGEN
  • MALLOC Debugging
  • MALLOC debugging
  • Manipulation of Conformation Files
  • Manipulations of Coordinates
  • Marking Atoms by Z Coordinate (Spheres)
  • Masking
  • Masses of Atoms
  • Matching of Comparison Data
  • MAXCUSD
  • MAXEVDW
  • MAXUSD
  • Memory Allocation
  • Memory Allocations
  • Memory Overlays
  • Memory Usage
  • Menu Items in Peer
  • Merging Conformation Files
  • Merging Trajectories
  • Messages from Compare Command
  • Meta-Syntax
  • Minimization
  • Miscellaneous Analysis Commands
  • MIX Strategy
  • Mixed Strategy
  • mkprocns
  • MKPROTO
  • MM Directory
  • MOD files
  • Modeling from torsion angles
  • Modeling Without Coordinates
  • Modifications to CONGEN
  • MOLD Program
  • Molecular Display
  • Molecular Drawings
  • Molecular Dynamics
  • Molecular Graphics
  • Molecular Surface
  • Mouse Buttons for Peer
  • Multiple Column Table Printing
  • Multipole Solvation Modeling
  • Multipole, Induced
  • Mutations

    n

  • n-Butane Dihedral
  • N-Methyl Acetamide
  • name
  • Name Translation
  • New Versions of CONGEN
  • Newton-Raphson Minimization
  • NMR Constraint File
  • NMR Constraint Printing
  • NMR Constraints
  • NOE Constraints
  • Non-bonded (NBOND) List
  • Non-bonded Energies
  • Non-bonded Energy
  • Non-bonded Exclusions
  • Non-bonded exclusions
  • Non-bonded Interaction Parameters
  • Non-bonded Interactions
  • Non-standard Fortran
  • `noproto.c'
  • Normal Mode Correlations
  • Normal Modes
  • NOT
  • NOTERMSYMMETRY
  • NTER residues
  • Number Properties
  • Number Sorting
  • Numeric Constants
  • Numeric Differences

    o

  • Open Files
  • Open Nodes
  • Opening Files
  • Operators on Selections
  • Optimization of Backbone Construction
  • Options and Operands
  • Ordering of Atoms
  • Organization of CONGEN
  • Orienting Coordinates
  • Origin of Data (Spheres)
  • Origin Shift for Sphere Drawing
  • Output
  • Output File
  • Output Files
  • Output from Dynamics
  • Overflow, Floating Point

    p

  • Pair Distance Computation
  • Pairing of Comparison Data
  • Parallel Execution
  • Parallel Processing
  • PARAM1
  • PARAM2
  • PARAM3
  • PARAM4
  • PARAM5
  • Parameter editing (IMP Command)
  • Parameter File Development
  • Parameter file format
  • Parameter File Reading
  • Parameter Files
  • Parameterization
  • Parameters
  • PARMALLH
  • PARMDNA1
  • PARMDNA3
  • PARMDNA4
  • PARMEXEL
  • PARMFIX10
  • PARMFIX2
  • PARMFIX5
  • PARMFIX7
  • PARMFIX8
  • PARMFIX9
  • Partial Charges
  • Patch Atom Charges
  • Patching
  • Patching Chain Termini
  • Patching Terminal Residues
  • Patterns for Atom Type Codes
  • PBE Energy History
  • PBE Printing
  • PBE Residuals
  • Peer File Format
  • Peptide isomerization
  • Periodic Images
  • Phi-Psi Plot
  • Phong Shading
  • Physical Memory
  • Pixel Size for Sphere Drawing
  • Placement of Table Statistics
  • PLOT Command
  • Plot Labels
  • Plotting
  • Plotting Time Series
  • PLT2
  • PLT2 Program
  • Pointers in Fortran
  • Poisson-Boltzmann Data Structures
  • Poisson-Boltzmann Electrostatics
  • Poisson-Boltzmann Energy
  • Poisson-Boltzmann Equation
  • Poisson-Boltzmann Equation I/O
  • Polarizability
  • Positional Constraints
  • Potential grid from IMP results
  • Potential, Electrostatic
  • Prerequisites for Energy Evaluations
  • Pretty Table Printing
  • Principal Axis Rotation
  • PRINHP
  • PRINSTK
  • Print Command Syntax
  • Print Sphere Drawing Parameters
  • PRINTE
  • Printing a File
  • Printing Files
  • Printing IMP values
  • Printing Sidechain Topology Files.
  • Printing Tables
  • Printing the PBE Data Structures
  • PRO.CNS
  • Process Name Setting
  • Programmer's interface
  • Programming Environment
  • Programming Languages
  • Programming Tools
  • Proline Constructor File
  • Proline Constructor File, `pro.cns'
  • Proline Constructors
  • Proline peptide isomerization
  • Proline Ring Construction
  • Properties in Tables
  • Properties of Atoms
  • property
  • Property Plotting
  • proring.inp
  • Protein Data Bank, Brookhaven
  • Protein Parameters
  • Protein Sequences
  • Protein Structure File
  • Protein Structure File (PSF)
  • Protein Structure File (PSF) Reading
  • Prototypes, ANSI C
  • Pruning the Search Tree
  • PSF
  • PSF editing
  • PSF's from a Sphere List

    q

  • QMAX
  • QMIN
  • Quadrupole Electrostatic Approximation
  • Queues
  • Queues in Conformational Search

    r

  • R-dependent Dielectric
  • Radii of Atom
  • Radii of Atoms
  • Radius for Surface Coloring
  • Radius Resetting for a Sphere Drawing
  • Radius Setting for Sphere Drawing
  • Ramachandran Plot
  • Random Structure Generation
  • Randomizing Coordinates
  • range
  • Range for Plotting
  • RBEST
  • RC
  • RCS
  • Reaction Field Properties
  • Read Best Degree of Freedom
  • Read Spheres
  • READDT
  • READDT Subroutine
  • Reading
  • Reading a Sequence
  • Reading Conformation Files
  • Reading Constraints
  • Reading coordinates
  • Reading dynamics trajectories
  • Reading Hydrogen Bonds
  • Reading Image Files
  • Reading Parameters
  • Reading Protein Structure Files (PSF)
  • Recalling saved IMPS results
  • Reference Coordinates
  • remappro
  • Removing Atoms from a Sphere Drawing
  • Reorienting a Coordinate Trajectory
  • Resetting a Time Series
  • Resetting colors for sphere drawings
  • Resetting Sphere Drawing
  • Residue Abbreviations
  • Residue Attributes
  • Residue by Residue non-bonded list construction
  • Residue Deletion in Tables
  • Residue Identifier (resid)
  • Residue Identifier (Resid)
  • Residue Matching
  • Residue Reading
  • Residue Topology File (RTF)
  • Residue Topology File Formats
  • Residue Topology Files
  • Residues
  • Residues in Sidechain Topologies
  • RESIZE
  • Resource Limits
  • REST
  • Restart File
  • Restart Files
  • Restarting Conformational Searches
  • Restore Previous Stream
  • Restraints
  • RETURN Command
  • Reuse of PBE Grids
  • Revision Control System
  • Rewind Files
  • RGB Format
  • Rigid Body Construction
  • Rigid Geometries
  • Root Mean Square (RMS) Calculation
  • Rotated Coordinate Writing
  • Rotating Coordinates
  • Rotation Matrix Input
  • Rotation of Coordinates
  • Rotation of Sphere Drawing
  • Rotation Origin (Spheres)
  • Round-off Error
  • RSS
  • RTF File Example
  • RTF File Formats
  • RTF File Printing
  • RTF Types
  • RTOP1
  • RTOP3
  • RTOP5
  • RTOP6
  • RTOP7
  • RTOP8
  • RTOPALLH3
  • RTOPALLH4
  • RTOPALLH5
  • RTOPALLH6
  • RTOPALLH7
  • RTOPDNA1
  • RTOPDNA3
  • RTOPDNA4
  • RTOPH2
  • RTOPH4
  • RTOPH5
  • RTOPH5A
  • RTOPH6
  • RTOPH7
  • RTOPH8
  • RUC
  • RUNCG

    s

  • Sampling of Conformations
  • Sampling of Degrees of Freedom
  • Saving IMPS results
  • Scaling Coordinates
  • Scaling for Sphere Drawing
  • Scaling Sphere Drawings
  • scanf functions
  • Scatter Plot
  • Scatter Plots
  • Search Command
  • Search Tree
  • Search Tree Pruning
  • Second Derivative Minimization
  • Segment Construction
  • Segment Deletion in Tables
  • Segment Identifier
  • Segment Identifier (SEGID's)
  • Segment Identifier (Segid)
  • Segment Matching
  • SELECT Command
  • selection
  • Selection of Atoms
  • Selection of Atoms for Sphere Drawing
  • Selection Operators
  • Selections
  • Sequence Deletions
  • Sequence Homology
  • Sequence Insertions
  • Sequence Splicing
  • Sequences
  • Setting Analysis Variables
  • SETUPI
  • Shading Spheres
  • Shake Command
  • Sharing File Access
  • Shell Command
  • Shell Commands
  • Shifted Electrostatic Potential
  • SHOW
  • Show Lighting Parameters
  • Show Sphere Drawing Parameters
  • Sidechain Construction
  • Sidechain grid
  • Sidechain Topology File
  • Sidechain Topology Files
  • Silicon Graphics RGB Format
  • Simulated Annealing
  • Size Limits
  • Sizing an Image for Sphere Drawing
  • Small Molecule Construction
  • Small Molecule Searches
  • Solvation
  • Solvation energy
  • Solvation Modeling
  • Solving an IMPS system
  • Sorting Files
  • Space Filling Drawing
  • Space Grid
  • Spacing Filling Displays
  • Spectral Radius for PBE Solution.
  • Specular Coefficient of Lighting
  • Sphere Drawing
  • Sphere Drawing Reset
  • Sphere Drawing Transformations
  • Sphere Lighting and Shading
  • Spheres List
  • Splice Command
  • Splicing Sequences
  • Splitting Conformation Files
  • Stack Management
  • Stack Size
  • Stacks
  • Standards for Code Writing
  • Static memory
  • Static Properties
  • Statistics, Adding to a Table
  • Status File
  • Status of Conformational Search
  • Steepest Descents
  • Stereo Offset for Sphere Drawing
  • Stern Layer
  • STKSIZ
  • Stopping Execution
  • Storage Management
  • Strategy for Conformational Search
  • Stream Switching
  • Stream, Returning to Previous
  • String to String Correction Problem
  • STRT
  • STRTDT
  • Structure of CONGEN
  • Support Program
  • Surface Areas, Atomic
  • Surface Normals
  • Surface, Accessible
  • Surface, Contact
  • Surface, Molecular
  • Surface, van der Waals
  • Swapping Coordinates
  • Switches for Peer
  • Symbol Table
  • Symbolic names
  • Symmetric Images
  • Syntax of Internal Coordinate Commands

    t

  • Table Classes
  • Table Cleaning
  • Table Commands
  • Table Data Plotting
  • Table I/O
  • Table Pretty Printing
  • Table Printing
  • Table Properties
  • Tables, Deleting Data from
  • tag
  • Tag Deletion in Tables
  • tag-pat
  • Tags
  • Terminal Residue Patching
  • Test Energy Derivatives
  • Test Internal Operations
  • Testing CONGEN
  • Testing the Poisson-Boltzmann Equation
  • Time Limits
  • Time Series
  • Time Series Manipulations
  • Time Series Plots
  • Time Series Resetting
  • Time-Series
  • Times for Execution
  • title
  • Title
  • Title Sphere Drawing
  • Tools for Programming
  • TOPCGEN file
  • Topology File Formats
  • Torsion Angle Energy
  • Torsion Angle Generation
  • Torsion Angle Maps
  • Torsion Angle Properties
  • Torsion Angle Specifications in the RTF
  • Torsion Angle, Complex
  • Torsion angles, building molecules from
  • Torsion Constraints
  • Trajectories
  • Trajectory Files, Correlation Functions
  • Trajectory Manipulation
  • Trajectory Merging
  • Trajectory Reorientation
  • Transform Inversion
  • Transformation of Coordinates
  • Transformations for Sphere Drawing
  • Transforming Atoms into Sphere List
  • Translated Coordinate Writing.
  • Translating Coordinates
  • Translation of Coordinates
  • Tree Pruning
  • Tree Search
  • `tree23.c'
  • Trilinear Interpolation
  • Twist Command
  • Twist of the Backbone
  • Type Array
  • Type Code Patterns

    u

  • Underflow Errors
  • Uniform Charging
  • unit-number
  • Units
  • Units of Measure
  • Unix Installation
  • Upper Case File Names
  • Usage
  • USEDDT
  • USER Command
  • User Energies
  • User Energy Functions
  • User variables
  • USERE
  • USERLINK
  • usermake
  • USERSB

    v

  • Value Deletion in Tables
  • Van der Waals Avoidance
  • Van der Waals Energies
  • Van der Waals Energy
  • Van der Waals Properties
  • Van der Waals Radius
  • Van der Waals Searches
  • Van der Waals Surface
  • Variables in Analysis
  • Variables, user
  • Vector Displays
  • Vector Drawings
  • VERL
  • Verlet Method
  • Versions of CONGEN, New
  • Vibrational Analysis
  • Virtual Memory Size
  • VMS Installation
  • Volumes, Atomic

    w

  • Warning Level Command
  • Water Molecules
  • Weight Command
  • Weighting Energies
  • Width of Output Files
  • word
  • Working Set
  • WRAPGEN
  • wrapgen
  • WRITDT
  • Write Image (Spheres)
  • Write Spheres
  • Writing Comparison Data
  • Writing Conformations from a Search
  • Writing Files

    x

  • XCONF

    z

  • Z Coordinate Marking (Spheres)
  • Z-buffer

    • Go to the previous section.