Concept Index

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1-4 Non-bonded Scaling: Parameter File Format
2DPlot Command: Scat
2DPLOT Command: 2DPlot Command
3TER residues: Read Sequence
5TER residues: Read Sequence
Ab initio Calculations: Gaussian Command
Abbreviations: Run Control
Abbreviations of Residues: Read Coordinates
Abbreviations of Residues: Read Sequence
ABI Specification: UNIX Installation
ABNR Minimization: Minimization
Acceptor (HB) Generation: Generate Command
Acceptors of Hydrogen Bonds in the RTF: RTF Acceptor Command
Accessible Surface: Gepol Command
Accessible Surface: Analysis Set Command
Accessible Surface: Atom Properties
Accessible Surface: Xconf Command
Accessible Surface: Selection Tokens
Accessible Surface Coloring: Atom Manipulations in Sphere Drawing
Accessible Surface Drawing: Overview of Sphere Drawing
ADD Command Syntax: Add Command Syntax
Adding Statistics to a Table: Adding Table Statistics
Adding Water Molecules: Read Sequence
Adopted Basis Newton-Raphson Minimization: Minimization
AKMA: AKMA
All Hydrogen Topology Files: RTOPALLH6
All Hydrogen Topology Files: RTOPALLH7
ALLCHP: Heaps
ALLCSTK: Stacks
ALLDT: Dynamic Data Structures
ALLHP: Heaps
Allocation of Dynamic Memory: Storage Management
ALLSTK: Stacks
Alpha Carbon Plots: General Draw Options
Alpha-carbon Displays: Peer Command
AMBER 94 parameters: AMBER94PARM
AMBER parameters: AMBERPARM
AMBER Potential: Parameter File Format
AMBER94RTF: AMBER94RTF
AMBERUNIRTF: AMBERUNIRTF
Amide Torsion Energy (AMBER94): AMBER94PARM
Amino Acid One Letter Code: Plot Command
Amino-isobutyric Acid (AIB): Chain Closure
Amino-isobutyric Acid (AIB): Backbone Degree of Freedom
Analysis Data I/O: I/O in Analysis
Analysis END Command: Analysis End Command
Analysis of Conformations: Cmploop
Analysis of Poisson-Boltzmann Electrostatics: Creation of Comparison Data
Analysis Set Command: Analysis Set Command
Analysis Twist Command: Analysis Twist Command
Analysis Variables: Analysis Set Command
AND: Operators on Selections
Angle Energies: Parameter File Format
Angle Generation: Generate Command
Angle Generation: RTF Generate Command
Angle Properties: Atom Properties
Angle Properties: Internal Coordinate Properties
Angle Specifications in the RTF: RTF Angle Command
Angles: Geometric Constants
Annealing: Dynamics
ANSI C Function Prototypes: Coding Standards
ANSI C Function Prototypes: Mkproto
Areas, Atomic Surface: IMP VOLUME
ASGNDT: Dynamic Data Structures
Atom Attribution of Poisson-Boltzmann Energy: Atom Properties
Atom Labeling: PLT2 Options for Draw
Atom Manipulations for Sphere Drawing: Atom Manipulations in Sphere Drawing
Atom Masses: RTF Mass Command
Atom Matching: Matching of Comparison Data
Atom Ordering: RTF Order Command
Atom Patch Charges: RTF Set Command
Atom Selection: Function of Coordinate Manipulations
Atom Selection: Merge CG Command
Atom Selection: Atom Selection
Atom Selection in Sphere Drawing: Overview of Sphere Drawing
Atom Selection Operators: Operators on Selections
Atom Specifications in the RTF: RTF Atom Command
Atom Static Properties: Atom Properties
Atom Type Code Patterns: Parameter File Format
Atomic Attribution of PBE Energy: PBE ENERGY Command
Atomic Charge: Atom Properties
Atomic Charges: Gaussian Command
Atomic Constraints: Harmonic Atom
Atomic Polarizability: Parameter File Format
Atomic Radii: AMBER94PARM
Atomic Radii: PBE SETUP Command
Atomic Surface Areas: IMP VOLUME
Atomic Volumes: IMP VOLUME
Atoms in Sidechain Topologies: Sidechain Topology
Attributes of Residues: Backbone and Chain Closure Overview
Attributes of Residues: RTF Attribute Command
Auto-Correlation Functions: Correlation Functions
autodoc: Tools
Automatic Generation: Generate Command
Automatic Generation: RTF Generate Command
Automatic Scaling for Sphere Drawing: Transformations for Sphere Drawing
Average Coordinate Writing: Analysis Write
Averaging Two Coordinates: Function of Coordinate Manipulations
Backbone Construction: Backbone Degree of Freedom
Backbone Construction Maps: Maps and Construction Tables
Backbone Construction Maps: Backbone Maps
Backbone Construction Order: Backbone Degree of Freedom
Backbone Degree of Freedom: Backbone and Chain Closure Overview
Backbone Energy Maps: Emap
Backbone Energy Maps: Backbone and Chain Closure Overview
Backbone Terminal Constructions: Backbone Degree of Freedom
Backbone Twist: Analysis Twist Command
Background Color for Spheres: Sphere Lighting
Base Array: Dynamic Data Structures
Binding Energy: PBE Example 1
Binding Energy Calculations: PBE SETUP Command
Bond Angle Energies: Parameter File Format
Bond Angle Specifications in the RTF: RTF Angle Command
Bond Angles: Geometric Constants
Bond Energies: Parameter File Format
Bond Lengths: Geometric Constants
Bond Properties: Atom Properties
Bond Properties: Internal Coordinate Properties
Bond Specifications in the RTF: RTF Bond Command
Boolean variables: Coding Standards
Boundary of Grid: PBE SETUP Command
Boundary, Electrostatic: Introduction to Poisson-Boltzmann Electrostatics
Brookhaven Protein Data Bank: Write Command
Brookhaven Protein Data Bank: Read Coordinates
Brookhaven Protein Data Bank: Read Sequence
Brookhaven to Congen Conversion: Brkchm
BUILD Command Syntax: Build Syntax
BUILD information: RTF File Formats
Builder Rule Generation: RTF Generate Command
Building CONGEN: Making CONGEN
Building from torsion angles: Data Structures
Building Tables: Building Tables
C: C
C Function Prototypes: Coding Standards
C Function Prototypes: Mkproto
C-terminus Construction: Backbone Degree of Freedom
Carbon Monoxide Patching: Patch Command
Cases of File Names: I/O Units
Cavity Energy: Gepol Command
Cavity Energy: Overview of Conformational Search
CG directory: Directory Names
CG Files: Conformation File
cg_new_node_q: Parallel Processing
cg_work_q: Parallel Processing
CGBIN directory: Directory Names
CGD directory: Directory Names
CGDATA directory: Directory Names
cgdefs: Making CONGEN
CGLIB directory: Directory Names
CGP directory: Directory Names
CGPLATFORM: Making CONGEN
cgprofile: Making CONGEN
CGPS directory: Directory Names
CGROOT Directory: Directory Names
CGS directory: Directory Names
CGT directory: Directory Names
CGTD directory: Directory Names
Chain Closure: Debug Command
Chain Closure: Chain Closure
Chain Closure: Backbone Degree of Freedom
Chain Closure: Backbone and Chain Closure Overview
Charge Calculation: PDGRID
Charge Calculation: PDM88
Charge on Atoms: Atom Properties
Charges: Introduction to Poisson-Boltzmann Electrostatics
Charges, Atomic: Gaussian Command
Charges, Patch Atoms: RTF Set Command
Checkpoint File: Checkpoint File
Checkpointing Conformational Searches: Checkpoint and Restart Options
Chemical Type Codes: RTF Mass Command
Chip Specification: UNIX Installation
Chiral Atoms (AMBER94): AMBER94PARM
Cis-Trans Peptide Isomerization: Chain Closure
Cis-Trans Peptide Isomerization: Backbone Degree of Freedom
Classes of Tables: Table Classes
Cleaning of Tables: Deletion from Standard Tables
Clearing the Sphere List: Data Flows for Drawing Spheres
Close Contact Searches: Close Contacts
Closing a File: Close Command
CLSCHN: Chain Closure
CLSCHN: Backbone and Chain Closure Overview
Clumps in Sidechain Topologies: Sidechain Topology
CO Parameters: PARAM2
Codes Command: Codes Command
Coding Rules for I/O: Coding Standards
Coding Standards: Coding Standards
Collection of Table Data: Collection of Table Data
Color Resetting for Sphere Drawings: Atom Manipulations in Sphere Drawing
Colors: Peer Command
Colors for Accessible Surface: Atom Manipulations in Sphere Drawing
Colors of Atoms for Sphere Drawing: Atom Manipulations in Sphere Drawing
Columnar Table Printing: Multiple Column Printing
Command Abbreviations: Run Control
Command files: Run Control
Comments: Run Control
Common Blocks: Overall Organization
Common Blocks: Data Structures
Common Blocks for Data Structures: Dynamic Data Structures
COMPARE Command Syntax: Compare Command Syntax
Comparing Coordinates: Function of Coordinate Manipulations
Comparison by Homology: Matching of Comparison Data
Comparison Coordinate Set: Function of Coordinate Manipulations
Comparison Coordinate Writing: Analysis Write
Comparison Coordinates: Creation of Comparison Data
Comparison Coordinates: Merge CG Command
Comparison coordinates: Read Coordinates
Comparison Data Structures: Creation of Comparison Data
Comparison Messages: Comparison Messages
Comparison of Conformations: Comparecmp
Comparison of Conformations: Comparecg
Comparison of Sequences: Splice Command
Comparison Tables: DIFF COMPARE Table Options
Comparisons: Comparisons
Comparisons of Conformations: Cmploop
Compiler Flags: Making CONGEN
Compiler Specification: UNIX Installation
config.h: Coding Standards
config.h: config.h
Conformation File Operations: Merge CG Command
Conformation File Reading: Xconf Command
Conformation Files: Xconf Command
Conformational Search: Debug Command
Conformational Search: Conformational Search
Conformational Search Examples: Examples of Conformational Search
Conformational Search I/O: Conformational Search Files
Conformational Search Limits: Conformational Search Limits
Conformational Search Method: Search Method Options
Conformational Search Related Commands: CONGEN Related
Conformational Search Strategy: Overview of Directed Searching
Conformational Search, Reducing Output: Evl Degree of Freedom
Conformational Search, Reducing Outputs: Write Degree of Freedom
Conformations File: Conformation File
CONGEN Command Syntax: Syntax of Conformational Search
Congen introduction: Introduction
CONGEN Modifications: Modifications
CONGEN Modifications: Energy Options
CONGEN Testing: Tests
Conjugate Gradient Minimization: Minimization
Conserved Residues: Matching of Comparison Data
Constant Dielectric: Non-bonded Algorithms
Constants of Geometry: Geometric Constants
Constants, Numeric: Coding Standards
Constraint Command: Energy Options
Constraint File for NMR: NMR Constraint File
Constraint Reading: Reading Other Files
Constraints: Atom Properties
Constraints: Splice Command
Constraints: Constraints
Constraints: Dynamics
Constraints: Data Structures
Construction of Backbone Energy Maps: Emap
Construction of Hydrogen Positions: HBUILD Command
Construction of Prolines: Emap
Construction of Small Molecules: Sidechain Topology
Construction of Tables: Building Tables
Construction of Unknown Positions: RTF Build Command
Contact Surface: Atom Properties
Contact Surface: Selection Tokens
Continuations lines: Run Control
Control: Run Control
Conversion of Brookhaven Formats: Brkchm
Conversion of peer files: Peercg
Conversion to SGI RGB Format: Sphrgb
Conversion, IMP to PBE: IMP TOGRID
Coordinate Averaging: Function of Coordinate Manipulations
Coordinate Comparison: Function of Coordinate Manipulations
Coordinate Constraints: Harmonic Atom
Coordinate Constraints: Energy Options
Coordinate Conversion, Brookhaven: Brkchm
Coordinate Copying: Function of Coordinate Manipulations
Coordinate Differences: Function of Coordinate Manipulations
Coordinate Displacement Arrays: Function of Coordinate Manipulations
Coordinate file format: Read Coordinates
Coordinate Fitting: Function of Coordinate Manipulations
Coordinate Initialization: Function of Coordinate Manipulations
Coordinate Manipulations: Coordinate Manipulations
Coordinate Matching: Matching of Comparison Data
Coordinate Orientation: Function of Coordinate Manipulations
Coordinate Properties: Atom Properties
Coordinate reading: Read Coordinates
Coordinate Rotation: Function of Coordinate Manipulations
Coordinate Scaling: Function of Coordinate Manipulations
Coordinate Swapping: Function of Coordinate Manipulations
Coordinate Transform Inversion: Function of Coordinate Manipulations
Coordinate Transforms: Function of Coordinate Manipulations
Coordinate Translation: Function of Coordinate Manipulations
Coordinates: Energy Needs
Coordinates: Data Structures
Coordinates after Conformational Search: Miscellaneous Global Options
Copying Coordinates: Function of Coordinate Manipulations
Copying RTF Residues: RTF Copy Command
Copying Sidechain Topology Residues: Sidechain Topology
Copyright Notices: Coding Standards
Core Dumps: Debug Command
Core size: Rlimit Command
Correlation Function Calculation: Calculating the Correlation Functions
Correlation Function Manipulations: Manipulating the Correlation Functions
Correlation Functions: Correlation Functions
CPK Models: Sphere Drawing
CPP: Fcpp
CPU Time for BUILD Command: Build Table Execution Time
CPU Time Limits: Rlimit Command
CPU Times: Time Command
Crystal Parameters: Function of Coordinate Manipulations
Crystallographic Images: Images
Crystallographic Images: Data Structures
CSTACK: Stacks
CSTKSIZ: Stacks
CTER residues: Read Sequence
Cut Data from a File: Extract
cutoffs, hydrogen bond: Hydrogen Bonds
Cutting a Sphere Drawing: Transformations for Sphere Drawing
Cutting a Sphere Drawing: Atom Manipulations in Sphere Drawing
Cyclic Peptides: Generate Command
D Amino Acids: Sidechain Topology
D Amino Acids: Backbone and Chain Closure Overview
D Amino Acids: RTF Attribute Command
D Amino Acids: RTF Copy Command
Dashed Lines: PLT2 Options for Draw
Data Deletion in Tables: Deletion from Standard Tables
Data Manipulation Commands: Data Manipulation Commands
Data Structures: Standard Files
Data Structures: Data Structures
Data Structures for Comparisons: Creation of Comparison Data
Data Structures for Non-bonded Interactions: Non-bonded Data Structures
Data Structures on the Heap: Dynamic Data Structures
Data Structures, Poisson-Boltzmann: PBE Data Structures
data-structure: Glossary
DBG_ALLSTK: Stacks
DCL commands: DCL or Shell Commands
DEANZA: DISPIMG
Debugging: Debug Command
Debugging a Conformational Search: Miscellaneous Global Options
Debye-Huckel Parameter: PBE SETUP Command
Debye-Huckel Parameter: Introduction to Poisson-Boltzmann Electrostatics
Deepening Evaluation Strategy: Overview of Directed Searching
Define Colors for Sphere Drawing: Atom Manipulations in Sphere Drawing
Degree of Freedom: Overview of Conformational Search
Deleting Data from Tables: Deleting from Tables
Deletion from Difference Tables: Deletion from Difference Tables
Deletions in a Sequence: Splice Command
delimiter: Syntactic Glossary
Delimiter Usage: Compare Command Syntax
Delimiters: Delim Command
Delimiters: Run Control
Depth First Search: Overview of Directed Searching
Derivatives of the Energy: Energy Derivative Test
DEVAL Search Strategy: Overview of Directed Searching
Device Setting for Sphere Command: Transformations for Sphere Drawing
DIE subroutine: Coding Standards
Dielectric Averaging: PBE SETUP Command
Dielectric Constant: Atom Properties
Dielectric Constant: PBE POTENTIAL Command
Dielectric Constant: PBE SETUP Command
Dielectric Smoothing: PBE SETUP Command
Difference in Coordinates: Function of Coordinate Manipulations
Difference Table Deletion: Deletion from Difference Tables
Difference Tables: DIFF COMPARE Table Options
Differences in Coordinates: Function of Coordinate Manipulations
Diffuse Coefficient of Lighting: Sphere Lighting
Dihedral Angle Energy: Parameter File Format
Dihedral Angle Properties: Atom Properties
Dihedral Angle Properties: Internal Coordinate Properties
Dihedral Angle Specifications in the RTF: RTF Torsion Command
Dihedral angles, building molecules from: Internal Coordinates
Dihedral Constraints: Debug Command
Dihedral Constraints: Splice Command
Dihedral Constraints: Miscellaneous Global Options
Dihedral Constraints: Harmonic Dihedrals
Dihedral Constraints: Energy Options
Dimensions of Sphere Drawing: Transformations for Sphere Drawing
Dipole Electrostatic Approximation: Non-bonded Algorithms
Dipole, Induced: IMP Command
Directed Conformational Search Example: Energy Directed Search Example
Directed Searching: Overview of Directed Searching
Directory Names: Directory Names
Display Lighting Parameters: Sphere Lighting
Display Sphere Drawing Parameters: Transformations for Sphere Drawing
Displaying Sphere Drawings: Displaying Sphere Drawings
Distance Computation: Distance Command
Disulfides: Disulfide Command
Division by Zero: Debug Command
DNA Parameter Files: PARMDNA4
DNA Parameters: Parameter Files
DNA Sequences: Read Sequence
DNA Topology Files: RTOPDNA4
Donor (HB) Generation: Generate Command
Donors for Hydrogen Bonds: Parameter File Format
Donors of Hydrogen Bonds in the RTF: RTF Donor Command
Double Precision: Coding Standards
Drawing Structures: Draw Command
DT_NUMERIC: Dynamic Data Structures
Dummy non-bonded Interactions: Non-bonded Algorithms
DUPLDT: Dynamic Data Structures
Dynamic Storage Allocation: Storage Management
Dynamics: Dynamics
Dynamics: Energy Manipulations
Dynamics trajectories, reading: Read Coordinates
Dynamics Trajectory Reorientation: Reorienting a Coordinate Trajectory
Editing Hydrogen Bonds: Edit Command
Editing the PSF: Edit Command
Editing topology files: RTF File Formats
Effective Number of Electrons: Atom Properties
Electrons, Effective Number: Atom Properties
Electrostatic Boundary: Introduction to Poisson-Boltzmann Electrostatics
Electrostatic Charges: Atom Properties
Electrostatic Interactions: Non-bonded Interactions
Electrostatic Potential: Introduction to Poisson-Boltzmann Electrostatics
Electrostatic Properties: Atom Properties
Electrostatics: Debug Command
Electrostatics: Poisson-Boltzmann Electrostatics
emap: Emap
emappro: Emap
EMAX variables: Maps and Construction Tables
END Command, Analysis: Analysis End Command
Ending Execution: Stop Command
Ending Sphere Drawing: Miscellaneous Sphere Drawing Commands
Energies with symmetric images.: Operation of Images
Energy Calculation Prerequisites: Energy Needs
Energy Calculations: Energy Manipulations
Energy Derivatives: Modifications
Energy Derivatives: Energy Derivative Test
Energy Directed Conformational Search Example: Energy Directed Search Example
Energy Evaluation Codes: Codes Command
Energy Maps: Backbone and Chain Closure Overview
Energy Properties: Atom Properties
Energy Weights: Weight Command
Energy, solvation: IMPS solvation
Ensemble Averaging: NMR Constraints
Environment Variables: Directory Names
Equilibrium Geometries: Geometric Constants
EQUIVALENCE Command: Function of Coordinate Manipulations
Error Handling: NoBomb Command
EVAL Search Strategy: Overview of Directed Searching
Evaluation of Conformations: Evl Degree of Freedom
Evaluation Strategy: Overview of Directed Searching
Evans and Sutherland Display: DI340
Example of Energy Directed Search: Energy Directed Search Example
Example of Five Residue Search: Example of Five Residue Search
Example of PBE in Conformational Search: PBE Example 2
Example of Sidechain Reconstruction: Complete Sidechain Reconstruction Example
Examples: Examples
Examples of Conformational Search: Examples of Conformational Search
Examples of Poisson-Boltzmann Usage: PBE Examples
Examples of Sphere Drawing: 1st Example Of Sphere Drawing
Examples, IMP Usage: IMP Examples
Exceptions, Floating Point: Debug Command
EXCH: Operators on Selections
EXCL: Operators on Selections
Exclusions from Non-bonded Interactions: Non-bonded Interactions
Execution Times: Time Command
Exiting from Sphere: Usage of Sphere Drawing
Expanded Nodes: Overview of Directed Searching
Explicit Hydrogen Topology Files: RTOPH7
Explicit Hydrogen Topology Files: RTOPH8
Extended Atom Topology Files: RTOP8
Extended Electrostatics: Non-bonded Algorithms
Extract Data from a File: Extract
Extracting Conformations: Xconf Command
F77 macros: Coding Standards
FCPP: Fcpp
File Closing: Close Command
File Name Cases: I/O Units
File Opening: Open Command
File Rewinding: Rewind Command
File Size Limit: Rlimit Command
Files Available: Standard Files
Files for Images: Files for Images
Filtering Conformers: Evl Degree of Freedom
Filtering Conformers: Write Degree of Freedom
Finite Difference Methods: PBE POTENTIAL Command
Finite Difference Methods: Introduction to Poisson-Boltzmann Electrostatics
Fitting of Coordinates: Function of Coordinate Manipulations
Fixed Atom Constraints: Splice Command
Fixed Atom Construction: Backbone Degree of Freedom
Fixed Atom Construction: Sidechain Overview
Fixed Atoms: Fixed Atoms
Fixed Atoms: Energy Options
Fixing Bond Lengths or Angles: Shake Command
Fixing Bonds and Angles: Energy Options
fixmake: Making CONGEN
FLECS: Fortran
Floating Point Exceptions: Debug Command
Flushing Output Buffers: Checkpoint and Restart Options
Force Constant: Parameter File Format
Force Constants: Tables for PARAM1
Force Constants: Force Constants
Force Drawing: Draw Command
Force Properties: Atom Properties
Format of coordinate files: Read Coordinates
Fortran: Fortran
Fortran C Preprocessor: Fcpp
Fortran Pointers: Coding Standards
Fractional Coordinates: Function of Coordinate Manipulations
FRECHP: Heaps
FRECSTK: Stacks
FREEDT: Dynamic Data Structures
FREHP: Heaps
FRESTK: Stacks
FSIZEOF: Stacks
Gamma Correction: SLU
Gaussian Program: PDGRID
Gaussian Program: PDM88
Gaussian Program: Gaussian Command
GEAR: Dynamics
Gear Method: Dynamics
Generate Command: Generate Command
Generating a Structure: Read Sequence
Generation of angles, torsions, etc.: RTF File Formats
Generation of Non-bonded Exclusions: Nbxmod
Generation of Non-bonded Interactions: Non-bonded Interactions
Generation of Residue Components: RTF Generate Command
Generation of Structures: Structure
Geometric Constants: Geometric Constants
GEPOL Calculation: Gepol Command
GEPOL Calculation: Atom Properties
GETE: CONGEN Modifications
Global Options for Conformational Search: Global Options for Conformational Search
Glossary: Syntactic Glossary
Glossiness for Spheres: Sphere Lighting
GNU Emacs: Fcpp
Go and Scheraga Procedure: Chain Closure
Go and Scheraga procedure: Backbone and Chain Closure Overview
Graphics: Molecular Graphics
GRID: Backbone Degree of Freedom
Grid Boundary: PBE SETUP Command
Grid Charging: PBE SETUP Command
Grid Dimension: PBE SETUP Command
GROUP Commmand: RTF Group Command
Harmonic Atom Constraints: Splice Command
Harmonic Constraints: Harmonic Atom
Harmonic Constraints: Energy Options
HDR: Coding Standards
Heap Management: Debug Command
Heap Storage: Heaps
HEME group patching: Patch Command
Heme Parameters: PARAM2
HISTO Command: Histo Command
Histograms: Histo
Histograms: Histo Command
Homologies: Matching of Comparison Data
Homology of Sequence: Homology
Hydrogen Bond (HBOND) List: Data Structures
Hydrogen Bond Acceptors in the RTF: RTF Acceptor Command
Hydrogen Bond Analysis: Print Command
Hydrogen Bond Donor/Acceptor Generation: Generate Command
Hydrogen Bond Donors in the RTF: RTF Donor Command
Hydrogen Bond Editing: Edit Command
Hydrogen Bond Energy: Parameter File Format
Hydrogen Bond Energy (AMBER94): AMBER94PARM
Hydrogen Bond Generation: Hydrogen Bonds
Hydrogen Bond Parameters: H-bonds and N-bonds
Hydrogen Bond Properties: Atom Properties
Hydrogen Bond Properties: Hydrogen Bond Properties
Hydrogen Bond Reading: Reading Other Files
Hydrogen Bonds: Creation of Comparison Data
Hydrogen Bonds: Splice Command
Hydrogen Bonds: Read Best Degree of Freedom
Hydrogen Bonds: Energy Calculation Options
Hydrogen Bonds: Energy Needs
Hydrogen Position Construction: HBUILD Command
I/O: I/O
I/O Coding Rules: Coding Standards
I/O for Conformational Search: Conformational Search Files
I/O for the Poisson-Boltzmann Equation: PBE WRITE Command
I/O for the Poisson-Boltzmann Equation: PBE READ Command
I/O in Analysis: I/O in Analysis
I/O of Atomic Constraints: Harmonic Atom
I/O with Tables: Table I/O
ICNTRL: Coding Standards
Identifier Deletion in Tables: Deletion from Standard Tables
Image (Spheres): Data Flows for Drawing Spheres
Image Files Reading: Reading Other Files
Image Format: Sphrgb
Image Sizing for Sphere Command: Transformations for Sphere Drawing
Images: Images
Images: Data Structures
Images, hydrogen bonds: Hydrogen Bonds
IMOVE array: Fixed Atoms
IMP usage examples: IMP Examples
Implementation of CONGEN: Implementation
Implementation of Non-bonded Interactions: Non-bonded Implementation
Improper Dihedrals: Internal Coordinates Concepts
Improper Torsion Angle Properties: Atom Properties
Improper Torsion Angle Properties: Internal Coordinate Properties
Improper Torsion Energies: Parameter File Format
Improper Torsion Energy: Parameter File Format
Improper Torsions in the RTF: RTF Improper Command
Index Common Block: Dynamic Data Structures
Induced Dipoles: IMP Command
Induced Multipoles: IMP Command
Inducible Multipole Solvation Modeling: IMP Command
Inexact Errors: Debug Command
INISTK: Stacks
INITDT: Dynamic Data Structures
INITHP: Heaps
Initialization of Coordinates: Function of Coordinate Manipulations
Initialization of Sphere Drawing: Usage of Sphere Drawing
Initialization of Sphere List: Data Flows for Drawing Spheres
Input: I/O
Input File: I/O Units
Input Rotation Matrix: Transformations for Sphere Drawing
Insertions in a Sequence: Splice Command
Installation of CONGEN on UNIX: UNIX Installation
Installation of CONGEN on VMS: VMS Installation
Interactive Display: Peer
Interfacing to CONGEN: CONGEN Modifications
Interlanguage Interface: Wrapgen
Internal Coordinate Command Syntax: Internal Coordinates Syntax
Internal Coordinate Concepts: Internal Coordinates Concepts
Internal Coordinate File Structure: Internal Coordinates Structure
Internal Coordinate Generation: RTF Generate Command
Internal Coordinate Properties: Internal Coordinate Properties
Internal Coordinates: Internal Coordinates
Internal Coordinates: Splice Command
Internal Coordinates: RTF File Formats
Internal Coordinates: Glossary
Internal Coordinates (IC): Data Structures
Internal Coordinates in the RTF: RTF Build Command
Invalid Floating Point Exceptions: Debug Command
Inversion of Coordinate Transforms: Function of Coordinate Manipulations
Ionic Strength: PBE SETUP Command
Iris 4D Display: Diris
Irix Specification: UNIX Installation
Iteration control (IMP Command): IMP SOLVE
Iteration control (IMP Command): IMP SETUP
IUPAC: Glossary
IUPAC: Syntactic Glossary
IUPAC Name Translations: Read Coordinates
J Coupling Constraints: Theory for J Coupling Constraints
J-coupling Constraints: Debug Command
J-coupling Constraints: Miscellaneous Global Options
J-coupling Constraints: NMR Constraints
Joined J coupling constraints: NMR Constraint File
Joined J Coupling Constraints: Theory for J Coupling Constraints
Karplus Equation: Theory for J Coupling Constraints
Keyboard Usage in Peer: Keyboard Usage in Peer
keyword: Syntactic Glossary
Konnert Hendrickson coordinate file format: Read Coordinates
Konnert-Hendrickson Format: Write Command
Labeling a Plot: PLT2 Options for Draw
Language Interface: Wrapgen
Least Squares Rotation and Translation: Matching of Comparison Data
Length Array: Dynamic Data Structures
Lighting of Spheres: Overview of Sphere Drawing
Lighting Range for Spheres: Sphere Lighting
Lighting Spheres: Sphere Lighting
Lighting Vector for Spheres: Sphere Lighting
Limits of Arrays: Size Limits
Line Drawings: Drawing
Line Width: Analysis Set Command
Linearized Poisson-Boltzmann equation: PBE POTENTIAL Command
Linkage Atom Naming: Linkage Atom Naming
Local Storage: Stacks
Log file: I/O Units
Log file: Run Control
Logical Names: Directory Names
Lower Case File Names: I/O Units
LSTCUSD: Stacks
LSTUSD: Stacks
Machine Directories: UNIX Installation
makefile.gen: Making CONGEN
Making a Sphere Drawing: Data Flows for Drawing Spheres
Making CONGEN: Making CONGEN
MALLOC debugging: Debug Command
MALLOC Debugging: Debug Command
Manipulation of Conformation Files: Merge CG Command
Manipulations of Coordinates: Coordinate Manipulations
Marking Atoms by Z Coordinate (Spheres): Transformations for Sphere Drawing
Marking Atoms by Z Coordinate (Spheres): Atom Manipulations in Sphere Drawing
Masking: PBE MASK Command
Masses of Atoms: RTF Mass Command
Matching of Comparison Data: Matching of Comparison Data
MAXCUSD: Stacks
MAXEVDW: Backbone Degree of Freedom
MAXUSD: Stacks
Memory Allocation: Storage Management
Memory Allocations: Debug Command
Memory Overlays: Fortran
Memory Usage: Rlimit Command
Menu Items in Peer: Pop-up Menu Items for Peer
Merging Conformation Files: Merge CG Command
Merging Trajectories: Manipulating Trajectories
Messages from Compare Command: Comparison Messages
Meta-Syntax: Meta-Syntax
Minimization: Energy Manipulations
MIPS Specification: UNIX Installation
Miscellaneous Analysis Commands: Analysis Miscellany
MIX Strategy: Overview of Directed Searching
Mixed Strategy: Overview of Directed Searching
mkprocns: Emap
MKPROTO: Mkproto
MM Directory: Directory Names
MOD files: Residue Topology Files
Modeling from torsion angles: Internal Coordinates
Modeling Without Coordinates: Internal Coordinates Concepts
Modifications to CONGEN: Modifications
Modifications to CONGEN: User Command
MOLD Program: Drawing
Molecular Display: Peer
Molecular Drawings: Drawing
Molecular Dynamics: Dynamics
Molecular Graphics: Molecular Graphics
Molecular Surface: Gepol Command
Molecular Surface: Atom Properties
Mouse Buttons for Peer: Mouse Buttons for Peer
Multiple Column Table Printing: Multiple Column Printing
Multipole Solvation Modeling: IMP Command
Multipole, Induced: IMP Command
Mutations: Matching of Comparison Data
n-Butane Dihedral: Tables for PARAM1
N-Methyl Acetamide: Tables for PARAM1
N-terminus Construction: Backbone Degree of Freedom
name: Syntactic Glossary
Name Translation: Read Coordinates
New Versions of CONGEN: New Versions
Newton-Raphson Minimization: Minimization
NMR Constraint File: NMR Constraint File
NMR Constraint Printing: Print Command
NMR Constraints: Debug Command
NMR Constraints: NMR Constraints
NOE Constraints: Theory for NOE Constraints
Non-bonded (NBOND) List: Data Structures
Non-bonded Energies: Parameter File Format
Non-bonded Energy: Parameter File Format
Non-bonded Exclusions: Nbxmod
Non-bonded exclusions: RTF Generate Command
Non-bonded Interaction Parameters: H-bonds and N-bonds
Non-bonded Interactions: Close Contacts
Non-bonded Interactions: Creation of Comparison Data
Non-bonded Interactions: Splice Command
Non-bonded Interactions: Energy Calculation Options
Non-bonded Interactions: Energy Needs
Non-bonded Interactions: Non-bonded Interactions
Non-standard Fortran: Fortran
noproto.c: Coding Standards
noproto.c: Mkproto
Normal Mode Correlations: Correlations on Normal Modes
Normal Modes: Function of Coordinate Manipulations
NOT: Operators on Selections
NOTERMSYMMETRY: Backbone Degree of Freedom
NTER residues: Read Sequence
Number Properties: Atom Properties
Number Sorting: Sortn
Numeric Constants: Coding Standards
Numeric Differences: Ndiffpost
Numeric Differences: Numdiff
Open Files: Rlimit Command
Open Nodes: Overview of Directed Searching
Opening Files: Open Command
Operators on Selections: Operators on Selections
Optimization of Backbone Construction: Backbone Degree of Freedom
Options and Operands: Run Control
Ordering of Atoms: RTF Order Command
Organization of CONGEN: Overall Organization
Orienting Coordinates: Function of Coordinate Manipulations
Origin of Data (Spheres): Transformations for Sphere Drawing
Origin Shift for Sphere Drawing: Transformations for Sphere Drawing
Output: I/O
Output File: I/O Units
Output Files: Analysis Set Command
Output from Dynamics: Dynamics Outputs
Overflow, Floating Point: Debug Command
Pair Distance Computation: Distance Command
Pairing of Comparison Data: Matching of Comparison Data
Parallel Execution: Rlimit Command
Parallel Processing: Comparecmp
Parallel Processing: Comparecg
Parallel Processing: Debug Command
Parallel Processing: Parallel Command
Parallel Processing: Poisson-Boltzmann Options
Parallel Processing: Search Method Options
Parallel Processing: Parallel Processing
Parallel Processing: PBE POTENTIAL Command
PARAM1: PARAM1
PARAM2: PARAM2
PARAM3: PARAM3
PARAM4: PARAM4
PARAM5: PARAM5
Parameter editing (IMP Command): IMP SETUP
Parameter File Development: PARAM1
Parameter file format: Param Files
Parameter File Reading: Reading Other Files
Parameter Files: Parameter Files
Parameterization: Force Constants
Parameters: Energy Needs
Parameters: Glossary
Parameters: Data Structures
PARMALLH: PARMALLH
PARMDNA1: PARMDNA1
PARMDNA3: PARMDNA3
PARMDNA4: PARMDNA4
PARMEXEL: PARMEXEL
PARMFIX10: PARMFIX10
PARMFIX2: PARMFIX2
PARMFIX5: PARMFIX5
PARMFIX7: PARMFIX7
PARMFIX8: PARMFIX8
PARMFIX9: PARMFIX9
Partial Charges: Gaussian Command
Patch Atom Charges: RTF Set Command
Patching: Patch Command
Patching Chain Termini: Read Sequence
Patching Terminal Residues: Generate Command
Patterns for Atom Type Codes: Parameter File Format
PBE Energy History: PBE POTENTIAL Command
PBE Printing: PBE DUMP Command
PBE Residuals: PBE POTENTIAL Command
Peer File Format: Peer
Peptide isomerization: Chain Closure
Peptide isomerization: Backbone Degree of Freedom
Periodic Images: Data Structures
Phi-Psi Plot: 2DPlot Command
Phong Shading: Overview of Sphere Drawing
Physical Memory: Rlimit Command
Pixel Size for Sphere Drawing: Transformations for Sphere Drawing
Placement of Table Statistics: Placement of Table Statistics
PLOT Command: Plot Command
Plot Labels: PLT2 Options for Draw
Plotting: Drawing
Plotting: Plotting
Plotting Time Series: Plotting Correlation Functions
PLT2: Draw Command
PLT2: PBE WRITE Command
PLT2 Program: Drawing
Pointers in Fortran: Coding Standards
Poisson-Boltzmann Data Structures: PBE Data Structures
Poisson-Boltzmann Electrostatics: Creation of Comparison Data
Poisson-Boltzmann Electrostatics: Poisson-Boltzmann Electrostatics
Poisson-Boltzmann Energy: Atom Properties
Poisson-Boltzmann Equation: Debug Command
Poisson-Boltzmann Equation: Poisson-Boltzmann Options
Poisson-Boltzmann Equation I/O: PBE WRITE Command
Poisson-Boltzmann Equation I/O: PBE READ Command
Polarizability: Atom Properties
Polarizability: Parameter File Format
Positional Constraints: Harmonic Atom
Positional Constraints: Energy Options
Potential grid from IMP results: IMP TOGRID
Potential, Electrostatic: Introduction to Poisson-Boltzmann Electrostatics
Prerequisites for Energy Evaluations: Energy Needs
Pretty Table Printing: Pretty Table Printing
Principal Axis Rotation: Function of Coordinate Manipulations
PRINHP: Heaps
PRINSTK: Stacks
Print Command Syntax: Print Command Syntax
Print Sphere Drawing Parameters: Transformations for Sphere Drawing
PRINTE: CONGEN Modifications
Printing a File: Print Command
Printing Files: Print Command
Printing IMP values: IMP PRINT
Printing Sidechain Topology Files.: Sidechain Topology
Printing Tables: Printing Tables
Printing the PBE Data Structures: PBE DUMP Command
PRO.CNS: Proline Constructors
Process Name Setting: Status Display Options
Programmer's interface: CONGEN Modifications
Programming Environment: Overall Organization
Programming Languages: Programming Environment
Programming Tools: Tools
Proline Constructor File: Proline Constructors
Proline Constructor File, pro.cns: Emap
Proline Constructors: Maps and Construction Tables
Proline peptide isomerization: Chain Closure
Proline peptide isomerization: Backbone Degree of Freedom
Proline Ring Construction: Backbone and Chain Closure Overview
Properties in Tables: Table Properties
Properties of Atoms: Atom Properties
property: Syntactic Glossary
Property Plotting: Drawing
proring.inp: Emap
Protein Data Bank, Brookhaven: Write Command
Protein Data Bank, Brookhaven: Read Coordinates
Protein Parameters: Parameter Files
Protein Sequences: Read Sequence
Protein Structure File: Splice Command
Protein Structure File: Structure
Protein Structure File (PSF): Energy Needs
Protein Structure File (PSF): Glossary
Protein Structure File (PSF): Data Structures
Protein Structure File (PSF) Reading: Reading Other Files
Prototypes, ANSI C: Coding Standards
Prototypes, ANSI C: Mkproto
Pruning the Search Tree: Tree Pruning Options
Pruning the Search Tree: Overview of Directed Searching
PSF: Structure
PSF editing: Edit Command
PSF's from a Sphere List: Overview of Sphere Drawing
QMAX: Parallel Processing
QMIN: Parallel Processing
Quadrupole Electrostatic Approximation: Non-bonded Algorithms
Queues: Search Method Options
Queues in Conformational Search: Parallel Processing
R-dependent Dielectric: Non-bonded Algorithms
Radii of Atom: PBE SETUP Command
Radii of Atoms: AMBER94PARM
Radius for Surface Coloring: Atom Manipulations in Sphere Drawing
Radius Resetting for a Sphere Drawing: Atom Manipulations in Sphere Drawing
Radius Setting for Sphere Drawing: Atom Manipulations in Sphere Drawing
Ramachandran Plot: 2DPlot Command
Random Structure Generation: Evl Degree of Freedom
Random Structure Generation: Overview of Directed Searching
Randomizing Coordinates: Function of Coordinate Manipulations
range: Syntactic Glossary
Range for Plotting: Plot Command
Range for Plotting: Histo Command
RBEST: Read Best Degree of Freedom
RC: DCL or Shell Commands
RCS: Programming Environment
Reaction Field Properties: Atom Properties
Read Best Degree of Freedom: Read Best Degree of Freedom
Read Spheres: Data Flows for Drawing Spheres
READDT: Dynamic Data Structures
READDT Subroutine: Analysis Read
Reading: Read Syntax
Reading a Sequence: Read Sequence
Reading Conformation Files: Xconf Command
Reading Constraints: Reading Other Files
Reading coordinates: Read Coordinates
Reading dynamics trajectories: Read Coordinates
Reading Hydrogen Bonds: Reading Other Files
Reading Image Files: Reading Other Files
Reading Parameters: Reading Other Files
Reading Protein Structure Files (PSF): Reading Other Files
Recalling saved IMPS results: IMP RECALL
Recalling saved IMPS results: IMP SAVE
Reference Coordinates: Merge CG Command
Reference Coordinates: Harmonic Atom
remappro: Emap
Removing Atoms from a Sphere Drawing: Atom Manipulations in Sphere Drawing
Reorienting a Coordinate Trajectory: Reorienting a Coordinate Trajectory
Resetting a Time Series: Resetting Time Series
Resetting colors for sphere drawings: Atom Manipulations in Sphere Drawing
Resetting Sphere Drawing: Transformations for Sphere Drawing
Residue Abbreviations: Read Coordinates
Residue Abbreviations: Read Sequence
Residue Attributes: Backbone and Chain Closure Overview
Residue Attributes: RTF Attribute Command
Residue by Residue non-bonded list construction: Non-bonded Algorithms
Residue Deletion in Tables: Deletion from Standard Tables
Residue Identifier (Resid): Glossary
Residue Identifier (resid): Syntactic Glossary
Residue Matching: Matching of Comparison Data
Residue Reading: Read Sequence
Residue Topology File (RTF): Glossary
Residue Topology File (RTF): Data Structures
Residue Topology File Formats: RTF File Formats
Residue Topology Files: Residue Topology Files
Residues: RTF Residue Command
Residues in Sidechain Topologies: Sidechain Topology
RESIZE: Dynamic Data Structures
Resource Limits: Rlimit Command
REST: Dynamics
Restart File: Dynamics
Restart Files: Energy Needs
Restarting Conformational Searches: Checkpoint and Restart Options
Restore Previous Stream: Return Command
Restraints: Constraints
RETURN Command: Return Command
Reuse of PBE Grids: PBE SETUP Command
Revision Control System: Programming Environment
Rewind Files: Rewind Command
RGB Format: Sphrgb
Rigid Body Construction: Backbone Degree of Freedom
Rigid Body Construction: Sidechain Overview
Rigid Geometries: Energy Options
Root Mean Square (RMS) Calculation: Function of Coordinate Manipulations
Rotated Coordinate Writing: Analysis Write
Rotating Coordinates: Function of Coordinate Manipulations
Rotation Matrix Input: Transformations for Sphere Drawing
Rotation of Coordinates: Matching of Comparison Data
Rotation of Sphere Drawing: Transformations for Sphere Drawing
Rotation Origin (Spheres): Transformations for Sphere Drawing
Round-off Error: Ndiffpost
Round-off Error: Numdiff
RSS: Rlimit Command
RTF File Example: Example RTF File
RTF File Formats: RTF File Formats
RTF File Printing: RTF Print Command
RTF Types: RTF Type Command
RTOP1: RTOP1
RTOP3: RTOP3
RTOP5: RTOP5
RTOP6: RTOP6
RTOP7: RTOP7
RTOP8: RTOP8
RTOPALLH3: RTOPALLH3
RTOPALLH4: RTOPALLH4
RTOPALLH5: RTOPALLH5
RTOPALLH6: RTOPALLH6
RTOPALLH7: RTOPALLH7
RTOPDNA1: RTOPDNA1
RTOPDNA3: RTOPDNA3
RTOPDNA4: RTOPDNA4
RTOPH2: RTOPH2
RTOPH4: RTOPH4
RTOPH5: RTOPH5
RTOPH5A: RTOPH5A
RTOPH6: RTOPH6
RTOPH7: RTOPH7
RTOPH8: RTOPH8
RUC: DCL or Shell Commands
RUNCG: DCL or Shell Commands
Sampling of Conformations: Overview of Conformational Search
Sampling of Degrees of Freedom: Overview of Directed Searching
Saving IMPS results: IMP RECALL
Saving IMPS results: IMP SAVE
Scaling Coordinates: Function of Coordinate Manipulations
Scaling for Sphere Drawing: Transformations for Sphere Drawing
Scaling Sphere Drawings: Transformations for Sphere Drawing
scanf functions: Coding Standards
Scatter Plot: 2DPlot Command
Scatter Plots: Scat
Search Command: Close Contacts
Search Tree: Overview of Directed Searching
Search Tree Pruning: Tree Pruning Options
Search Tree Pruning: Overview of Directed Searching
Second Derivative Minimization: Minimization
Segment Construction: Generate Command
Segment Deletion in Tables: Deletion from Standard Tables
Segment Identifier: Syntactic Glossary
Segment Identifier (SEGID's): Generate Command
Segment Identifier (Segid): Glossary
Segment Matching: Matching of Comparison Data
SELECT Command: Select Command
selection: Select Command
Selection of Atoms: Atom Selection
Selection of Atoms for Sphere Drawing: Atom Manipulations in Sphere Drawing
Selection Operators: Operators on Selections
Selections: Select Command
Selections: Plotting
Sequence Deletions: Splice Command
Sequence Homology: Homology
Sequence Insertions: Splice Command
Sequence Splicing: Splice Command
Sequences: Generate Command
Setting Analysis Variables: Analysis Set Command
SETUPI: Dynamic Data Structures
Shading Spheres: Sphere Lighting
Shake Command: Energy Options
Sharing File Access: I/O Units
Shell Command: Shell Command
Shell Commands: DCL or Shell Commands
Shifted Electrostatic Potential: Non-bonded Algorithms
SHOW: Operators on Selections
Show Lighting Parameters: Sphere Lighting
Show Sphere Drawing Parameters: Transformations for Sphere Drawing
Sidechain Construction: Torsion Energy Minimum Test
Sidechain Construction: Sidechain Degree of Freedom
Sidechain Construction: Sidechain Overview
Sidechain grid: Torsion Energy Minimum Test
Sidechain Topology File: Sidechain Topology
Sidechain Topology Files: Maps and Construction Tables
Silicon Graphics RGB Format: Sphrgb
Simulated Annealing: Dynamics
Size Limits: Size Limits
Sizing an Image for Sphere Drawing: Transformations for Sphere Drawing
Small Molecule Construction: Sidechain Topology
Small Molecule Searches: Overview of Conformational Search
Solvation: Poisson-Boltzmann Electrostatics
Solvation energy: IMPS solvation
Solvation Modeling: IMP Command
Solving an IMPS system: IMP SOLVE
Sorting Files: Sortn
Space Filling Drawing: Sphere Drawing
Space Grid: Debug Command
Spacing Filling Displays: Peer
Spectral Radius for PBE Solution.: PBE POTENTIAL Command
Specular Coefficient of Lighting: Sphere Lighting
Sphere Drawing: Sphere Drawing
Sphere Drawing Reset: Transformations for Sphere Drawing
Sphere Drawing Transformations: Transformations for Sphere Drawing
Sphere Lighting and Shading: Sphere Lighting
Spheres List: Overview of Sphere Drawing
Splice Command: Usage of Sphere Drawing
Splicing Sequences: Matching of Comparison Data
Splicing Sequences: Splice Command
Splitting Conformation Files: Merge CG Command
Stack Management: Debug Command
Stack Size: Rlimit Command
Stacks: Stacks
Standards for Code Writing: Coding Standards
Static memory: Coding Standards
Static Properties: Table Properties
Statistics, Adding to a Table: Adding Table Statistics
Status File: Status File
Status of Conformational Search: Status Display Options
Steepest Descents: Minimization
Stereo Offset for Sphere Drawing: Transformations for Sphere Drawing
Stern Layer: PBE SETUP Command
STKSIZ: Stacks
Stopping Execution: Stop Command
Storage Management: Storage Management
Strategy for Conformational Search: Overview of Directed Searching
Stream Switching: Analysis Set Command
Stream Switching: Stream Command
Stream, Returning to Previous: Return Command
String to String Correction Problem: Matching of Comparison Data
STRT: Dynamics
STRTDT: Dynamic Data Structures
Structure of CONGEN: Overall Organization
Support Program: Support
Surface Areas, Atomic: IMP VOLUME
Surface Normals: Sphere Lighting
Surface, Accessible: Gepol Command
Surface, Accessible: Analysis Set Command
Surface, Accessible: Atom Properties
Surface, Accessible: Xconf Command
Surface, Contact: Atom Properties
Surface, Molecular: Gepol Command
Surface, Molecular: Atom Properties
Surface, van der Waals: Gepol Command
Surface, van der Waals: Atom Properties
Swapping Coordinates: Function of Coordinate Manipulations
Switches for Peer: Switches for Peer
Symbol Table: PBE SAVE Command
Symbolic names: IMP PRINT
Symmetric Images: Images
Syntax of Internal Coordinate Commands: Internal Coordinates Syntax
Table Classes: Table Classes
Table Cleaning: Deletion from Standard Tables
Table Commands: Tables
Table Data Plotting: Drawing
Table I/O: Table I/O
Table Pretty Printing: Pretty Table Printing
Table Printing: Printing Tables
Table Properties: Table Properties
Tables, Deleting Data from: Deleting from Tables
tag: Syntactic Glossary
Tag Deletion in Tables: Deletion from Standard Tables
tag-pat: Select Command
Tags: Table Classes
Terminal Residue Construction: Backbone Degree of Freedom
Terminal Residue Patching: Generate Command
Test Energy Derivatives: Energy Derivative Test
Test Internal Operations: Test Command
Testing CONGEN: Tests
Testing the Poisson-Boltzmann Equation: PBE TEST Command
Time Limits: Rlimit Command
Time Series: Time Series
Time Series Manipulations: Manipulating Time Series
Time Series Manipulations: CORREL Command Manipulations
Time Series Plots: Plotting Correlation Functions
Time Series Resetting: Resetting Time Series
Time-Series: Correlation Functions
Times for Execution: Time Command
title: Syntactic Glossary
Title: Run Control
Title Sphere Drawing: Data Flows for Drawing Spheres
Tools for Programming: Tools
TOPCGEN file: Sidechain Topology
Topology File Formats: RTF File Formats
Torsion Angle Energy: Torsion Energy Minimum Test
Torsion Angle Energy: Parameter File Format
Torsion Angle Generation: Generate Command
Torsion Angle Generation: RTF Generate Command
Torsion Angle Maps: Backbone Maps
Torsion Angle Properties: Atom Properties
Torsion Angle Properties: Internal Coordinate Properties
Torsion Angle Specifications in the RTF: RTF Torsion Command
Torsion Angle, Complex: RTF Torsion Command
Torsion angles, building molecules from: Internal Coordinates
Torsion Constraints: Debug Command
Torsion Constraints: Miscellaneous Global Options
Torsion Constraints: Harmonic Dihedrals
Torsion Constraints: Energy Options
Trajectories: Dynamics
Trajectory Files, Correlation Functions: Files for Correlation Functions
Trajectory Manipulation: Manipulating Trajectories
Trajectory Merging: Manipulating Trajectories
Trajectory Reorientation: Reorienting a Coordinate Trajectory
Transform Inversion: Function of Coordinate Manipulations
Transformation of Coordinates: Function of Coordinate Manipulations
Transformations for Sphere Drawing: Transformations for Sphere Drawing
Transformations for Sphere Drawing: Overview of Sphere Drawing
Transforming Atoms into Sphere List: Data Flows for Drawing Spheres
Translated Coordinate Writing.: Analysis Write
Translating Coordinates: Function of Coordinate Manipulations
Translation of Coordinates: Matching of Comparison Data
Tree Pruning: Tree Pruning Options
Tree Pruning: Overview of Directed Searching
Tree Search: Overview of Directed Searching
tree23.c: Mkproto
Trilinear Interpolation: PBE SETUP Command
Twist Command: Analysis Twist Command
Twist of the Backbone: Analysis Twist Command
Type Array: Dynamic Data Structures
Type Code Patterns: Parameter File Format
Underflow Errors: Debug Command
Uniform Charging: PBE SETUP Command
unit-number: Syntactic Glossary
Units: I/O Units
Units: Run Control
Units of Measure: AKMA
Unix Installation: UNIX Installation
update_tree: Making CONGEN
Upper Case File Names: I/O Units
Usage: Usage
USEDDT: Dynamic Data Structures
USER Command: User Command
User Energies: Atom Properties
User Energy Functions: Evl Degree of Freedom
User variables: IMP PRINT
USERE: CONGEN Modifications
USERLINK: CONGEN Modifications
usermake: CONGEN Modifications
USERSB: CONGEN Modifications
Value Deletion in Tables: Deletion from Standard Tables
Van der Waals Avoidance: Vavoid Hydrogen Bond Test
Van der Waals Avoidance: Sidechain Overview
Van der Waals Energies: Parameter File Format
Van der Waals Energy: Parameter File Format
Van der Waals Properties: Atom Properties
Van der Waals Radius: Atom Properties
Van der Waals Searches: Close Contacts
Van der Waals Surface: Gepol Command
Van der Waals Surface: Atom Properties
Variables in Analysis: Analysis Set Command
Variables, user: IMP PRINT
Vector Displays: Peer
Vector Drawings: Drawing
VERL: Dynamics
Verlet Method: Dynamics
Versions of CONGEN, New: New Versions
Vibrational Analysis: Force Constants
Virtual Memory Size: Rlimit Command
VMS Installation: VMS Installation
Volumes, Atomic: IMP VOLUME
Warning Level Command: Wrnlev Command
Water Molecules: Read Sequence
Weight Command: Energy Options
Weighting Energies: Weight Command
Width of Output Files: Analysis Set Command
word: Syntactic Glossary
Working Set: Rlimit Command
wrapgen: Coding Standards
WRAPGEN: Wrapgen
WRITDT: Dynamic Data Structures
Write Image (Spheres): Data Flows for Drawing Spheres
Write Spheres: Data Flows for Drawing Spheres
Writing Comparison Data: Analysis Write
Writing Conformations from a Search: Write Degree of Freedom
Writing Files: Write Command
XCONF: Debug Command
Z Coordinate Marking (Spheres): Transformations for Sphere Drawing
Z Coordinate Marking (Spheres): Atom Manipulations in Sphere Drawing
Z-buffer: Overview of Sphere Drawing