Index

statement: Syntax
( ): Notation
1-4 interaction: Syntax | Syntax | Syntax | Syntax | Files “parhcsdx.pro" and “tophcsdx.pro" | Intramolecular Interactions
:==: Notation
: Notation
* *: Notation
: Words
* *: Wildcards
@: Control Statements
@@: Control Statements
{}: Words
|: Notation
accessible surface area: Accessible Surface Area
angle database restraint: Angle Database Restraint
ANGLedb-statement: Syntax
ANIS statement: Syntax - ANIS
anomalous scattering: Anomalous Scattering
antidistance restraints: Antidistance Restraints
application: Control Statements | Application Statements
atom properties: Syntax
atom selection: Atom Selection
atom selection, fragile: Atom Selection
atom tag: Syntax | Conformation vs. Residue Number
atom-based parameters: Parameter Statement | Examples of Atom-based Modifications
atomic form factors: Syntax of the Xrefin
B-factor refinement: Overall B-Factor Refinement | Individual B-Factor Refinement
Backus-Naur notation: Notation
bond angle deviations: Example: Print Bond Length
bond length deviations: Example: Print Bond Length
bound smoothing: Bound Smoothing
boundary forces, deformable: Deformable Boundary Forces
Brookhaven Protein Data Bank: Syntax
building,hydrogens: Building Hydrogen Positions
carbohydrates,topologies and parameters: Files “toph3.cho" and “param3.cho"
carbon chemical shift: Carbon Chemical Shift Restraints
CARBon shift statement: Syntax
centroid search: Intramolecular Interactions
CHARMM trajectory format: Binary Trajectory Files
chemical shift anisotropy restraint: Chemical Shift Anisotropy Restraint
chemical shift, carbon: Carbon Chemical Shift Restraints
chemical shift, proton: Proton Chemical Shift Restraints
chiral centers: Test for the Correct
chirality: Conformational Energy Terms | NMR Structure Determination
chromophores,topologies and parameters: Files “toph19.chromo" and “param19.chromo"
COLLapse-statement: Syntax
completeness of diffraction data: Syntax of the Xrefin
conformational analysis: Conformation vs. Residue Number
conjugate gradient minimization: Conjugate Gradient Minimization
constraints interaction statement: Energy Calculation between Selected
constraints,coordinate: Coordinate Constraints
constraints,fixing atomic positions: Fixing Atomic Positions
constraints,fixing distances: Fixing Distances
constraints,SHAKE: Fixing Distances
control statement: Control Statements
coordinates: Cartesian Coordinates
coordinates, fractionalization: Examples | Orthogonalization Convention
coordinates, orthogonalization: Examples | Orthogonalization Convention
coordinates, unknown: What to Do about
coordinates,best fit: Syntax
coordinates,comparison set: Syntax
coordinates,manipulating: Coordinate Statement
coordinates,rms difference: Syntax
coordinates,rms difference (rmsd) analysis: Rms Differences between Coordinates
coordinates,rms difference analysis: Average Structure and Rmsds
coordinates,rms difference,pairwise: Pairwise Rmsds
coordinates,rotation and translation: Syntax
coordinates,writing: Write Coordinate Statement
COUPlings statement: Syntax
crystal packing: Deviations from Ideality and
crystallographic diffraction data: Syntax of the Xrefin
crystallographic refinement: Crystallographic Refinement
crystallographic refinement, atomic positions: Positional Refinement
crystallographic refinement, simulated annealing: Crystallographic Refinement by Simulated
crystallographic refinement, B-factors: Overall B-Factor Refinement | Individual B-Factor Refinement
crystallographic refinement,alternate conformations,disorder: Alternate Conformations
crystallographic refinement,bad contacts: Check of Data and
crystallographic refinement,initial structure check: Check of Data and
crystallographic refinement,linear correlation coefficient: Crystallographic Target Functions
crystallographic refinement,occupancies: Grouped B-Factor and Occupancy
crystallographic refinement,overview: Crystallographic Refinement
crystallographic refinement,phase accuracy: Cross-validation: The Free
crystallographic refinement,slow-cooling: Crystallographic Refinement by Simulated
crystallographic refinement,special positions: Special Positions
crystallographic refinement,target functions: Crystallographic Target Functions
crystallographic refinement,topologies and parameters: Files “parallhdg.pro" and “topallhdg.pro"
crystallographic refinement,weights: Check of Data and
CSA restraint: Chemical Shift Anisotropy Restraint
DANI-statement: Syntax
database restraints, dihedral: Dihedral Angle Database Restraints
database restraints, positional: Residue-Residue Position/Orientation Database Restraint
DCSA-statement: Syntax
deformable boundary forces: Deformable Boundary Forces
deletion of atoms: Deleting Atoms
deviation from ideality: Deviations from Ideality and
diffraction data: Crystallographic Diffraction Data
diffraction data, completeness: Syntax of the Xrefin
diffraction data, expanding: Example: Expand a Data
diffraction data, reducing: Example: Expand a Data
diffraction data,manipulation: Manipulating Reflection Data
diffraction data,scaling: Crystallographic Target Functions | Syntax
diffusion anisotropy restraints: Diffusion Anisotropy Restraints
dihedral angle restraints: Dihedral Angle Restraints
dihedral restraints, database: Dihedral Angle Database Restraints
dipolar couplings: Residual Dipolar Couplings
DIPOlar statement: Syntax - XDIPolar or
directory environment variables: Commonly used UNIX variables
display: Control Statements
distance geometry,van der Waals interactions: Input Distances
distance analysis: Analysis of the Nonbonded
distance difference matrix: Distance Matrix Analysis
distance geometry: Distance Geometry | Implementation of Distance Geometry
distance geometry, accuracy parameter: Input Distances
distance geometry,bond angle constraints: Input Distances
distance geometry,bound smoothing: Bound Smoothing
distance geometry,dihedral angle constraints: Input Distances
distance geometry,distance bounds: Input Distances
distance geometry,embedded substructures: Distance Geometry
distance geometry,embedding: Embedding
distance geometry,full-structure embedding: Full-Structure Distance Geometry
distance geometry,improper angle constraints: Input Distances
distance geometry,metrization: Metrization
distance geometry,pseudoatoms: Pseudoatoms
distance geometry,regularization of coordinates: Regularization
distance geometry,rigid group: Syntax
distance geometry,SA-regularization of structures: SA-Regularization of DG-Structures
distance geometry,scaling: Scaling
distance geometry,triangle inequalities: Bound Smoothing
distance matrix: Distance Matrix Analysis
distance restraints: Distance Restraints
distance restraints, restraining functions: Choice of Restraining Functions
distance restraints,ambiguous: Expressing ambiguous restraints using
distance restraints,averaging methods: Choice of Averaging
distance restraints,disulfide bonds: Incorporation of Other Distance
distance restraints,hydrogen bonds: Incorporation of Other Distance
distance restraints,reading: Setup of Distance Restraints
distance,between atoms: Example: Pick Distance between
disulfide bridge: Example: Incorporation of Disulfide
disulfide bridges: NMR Structure Determination
duplicating the molecular structure: Duplicating the Molecular Structure
electron density map: Electron Density Maps
electron density map, $2F_{obs}-F_{calc}$ map: Example: Computation of a
electron density map,map file: Electron Density Map File
electron density map,omit map: Example: Computation of an
electron density map,SA-refined omit map: Example: Computation of an
embedding: Embedding
empirical energy function: Empirical Energy Functions
energy analysis, conformational terms: Geometric and Energetic Analysis
energy analysis,nonbonded terms: Analysis of the Nonbonded
energy analysis,setting the weight: Syntax
energy evaluation: Energy Statement
energy function: Energy Function | Empirical Energy Functions
energy minimization: Energy Minimization
energy, bond: Conformational Energy Terms
energy, bond angle: Conformational Energy Terms
energy, conformational: Conformational Energy Terms
energy, dihedral angle: Conformational Energy Terms
energy, electrostatic: Electrostatic Function
energy, hydrogen bond: The Explicit Hydrogen-Bond Term
energy, improper angle: Conformational Energy Terms
energy, nonbonded: Nonbonded Energy Terms
energy, torsion angle: Conformational Energy Terms
energy, van der Waals: Van der Waals Function
energy,analysis: Energy Calculation between Selected
energy,crystallographic symmetry: Crystallographic Symmetry Interactions
energy,interaction between selected atoms: Energy Calculation between Selected
energy,intermolecular: Crystallographic Symmetry Interactions | Non-crystallographic Symmetry Interactions
energy,intramolecular: Intramolecular Interactions
energy,non-crystallographic symmetry: Non-crystallographic Symmetry Interactions
energy,pick: Syntax of the Pick
energy,print: Syntax of the Print
energy,second function: Energy Calculation between Selected | Syntax
energy,turning on or off: Turning Energy Terms On
equal sign: Notation
Eulerian angles: 3 $\times$ 3 Matrices
evaluate: Evaluate Statement
example files,on-line: Electronic Location of Example
fast Fourier transformation: Crystallographic Target Functions | Syntax of the Xrefin
figure of merit: Crystallographic Target Functions | Syntax of the Xrefin | Syntax
filenames: Filenames
flags: Turning Energy Terms On
for ...in: Control Statements
force-field: Topology and Parameter Files
fractional coordinates: Orthogonalization Convention
fractionalized coordinates: Examples
fragile atom selection: Atom Selection
free value: Cross-validation: The Free
Friedel mates: Syntax of the Xrefin
geometric analysis: Geometric and Energetic Analysis | Deviations from Ideality and
geometry,pick: Syntax of the Pick
geometry,print: Syntax of the Print
harmonic restraints: Harmonic Coordinate Restraints
HBDA-statement: Syntax
HBDB-statement: Syntax
heavy-side function: Syntax
help on-line: On-line HELP and Query
histidine protonation: Example: Modification of the
hydrogen bond database restraint: Hydrogen Bond Database Restraint
hydrogen bond geometry restraint: Hydrogen Bond Geometry Restraint
hydrogen building: Building Hydrogen Positions
hydrogen-bond donors and acceptors: The Explicit Hydrogen-Bond Term
hydrogen-bonding parameters: Syntax
hydrogens: Syntax | Building Hydrogen Positions
hydrogens,naming convention: Convention for Hydrogen Names
if ...then: Control Statements
inertia tensor: Rigid-Body Coordinate Space
interchain interaction energy: Example: Interchain Interaction Energy
intramolecular interactions: Intramolecular Interactions
j-coupling restraints: Scalar J-Coupling Restraints
Langevin dynamics: Simple Langevin Dynamics | Example: Run Langevin Dynamics
Lattman's angles: 3 $\times$ 3 Matrices
learning parameters: no title | Learning Atom-based Parameters
Lee and Richards algorithm: Accessible Surface Area
Lennard-Jones potential: Nonbonded Energy Terms | Van der Waals Function
letters,uppercase and lowercase: Notation
lipids,topologies and parameters: CHARMM “top_all22*" and “par_all22*"
loops: Example: A Simple Loop | Example: A Double Loop | Example: Switch Control to
Luzzati plot: Luzzati Plot
manipulating coordinates: Coordinate Statement
manipulation,diffraction data: Manipulating Reflection Data
Mathematica: Mathematica Interface
matrices: 3 $\times$ 3 Matrices
Maxwellian distribution function: Syntax
messages: Set Statement
metrix matrix distance geometry: Distance Geometry
metrization: Metrization
minimization: Energy Minimization
minimization,conjugate gradient: Conjugate Gradient Minimization
minimization,rigid-body: Rigid-Body Minimization
mirror images: Test for the Correct
molecular dynamics: Molecular Dynamics
molecular dynamics,angular distribution: Angular Distribution Functions
molecular dynamics,average displacement: Average Coordinates and Fluctuations
molecular dynamics,covariance: Covariance Analysis
molecular dynamics,density: Density Analysis
molecular dynamics,finite difference approximation: Finite Difference Approximation
molecular dynamics,merging files: Merging Trajectories
molecular dynamics,orienting trajectory frames: Syntax
molecular dynamics,pick properties: Picking Properties for Trajectories
molecular dynamics,power spectrum: Power Spectrum Analysis
molecular dynamics,radial distribution function: Radial Distribution Functions
molecular dynamics,restarts: Dynamics Restarts
molecular dynamics,simulation: Example: Run a Standard | Example: Run a Molecular | Example: Run a Slow-cooling
molecular dynamics,slow-cooling: Example: Run a Slow-cooling
molecular dynamics,temperature control: Temperature Control
molecular dynamics,temperature control,Langevin dynamics: Langevin Dynamics
molecular dynamics,temperature control,temperature coupling: Temperature Coupling
molecular dynamics,temperature control,velocity rescaling: Velocity Rescaling
molecular dynamics,time correlation: Time Correlation Analysis
molecular dynamics,trajectories: Management of Trajectories
molecular dynamics,trajectory analysis: Analysis of Trajectories
molecular dynamics,velocity assignment: Velocity Assignment
molecular replacement: Molecular Replacement
molecular replacement,cluster analysis: The Rotation Function Listing
molecular replacement,cluster criteria: Rotation Search
molecular replacement,comparing rotation matrices: Comparing Orientations of Molecules
molecular replacement,contour plots: A Mathematica Script File
molecular replacement,cross rotation function,PC-refinement: PC-Refinement of the Highest | Analysis of the PC-refinement
molecular replacement,cross-rotation function: Cross-Rotation Function with the
molecular replacement,direct rotation function: A “Direct" Rotation Function
molecular replacement,elbow angle modification: Modification of the Elbow
molecular replacement,packing function: A Packing Function
molecular replacement,rigid-body refinement: Rigid-Body Refinement
molecular replacement,rotation search: Rotation Search
molecular replacement,self-rotation function: Self-rotation Function
molecular replacement,translation function,asymmetric unit: Translation Search
molecular replacement,translation function,finding second molecule: Translation Function for Molecule
molecular replacement,translation function,relative position: Combined Translation Function to
molecular replacement,translation function,using -refined model: Translation Function for Molecule
molecular replacement,translation search: Translation Search
molecular structure file: Example: How to Read
molecular structure,append: Example: Append Two Molecular
molecular structure,deletion: Deleting Atoms
molecular structure,disulfide bridge: Example: Incorporation of Disulfide
molecular structure,duplicating: Duplicating the Molecular Structure
molecular structure,examples: Examples for Molecular Structure
molecular structure,generation: Generating the Molecular Structure
molecular structure,histidine protonation: Example: Modification of the
molecular structure,incomplete polypeptide chain: Example: A Polypeptide Chain
molecular structure,nucleic acid: A Nucleic Acid Structure
molecular structure,patching: Syntax | Patching the Molecular Structure
molecular structure,polypeptide chain: Example: A Polypeptide Chain
molecular structure,protein: A Standard Protein Structure
molecular structure,protein,unusual geometries: How to Set Up
molecular structure,reading: Structure Statement
molecular structure,sequence: Syntax
molecular structure,solvent and solute: Example: Solvation of a
molecular structure,unknown atoms: What to Do about
molecular structure,viruses or multimers: Virus Structures or Structures
molecular structure,water: Example: Water Molecules
molecular structure,writing: Writing a Molecular Structure
NCS: Non-crystallographic Symmetry | Strict NCS
Newton's equations of motion: Molecular Dynamics
NMR relaxation refinement, value: Assessing the Quality of
NMR relaxation refinement,against NOESY intensities: Refinement against NOESY Intensities
NMR relaxation refinement,cutoffs: Cutoffs
NMR relaxation refinement,including solvent spectra: Simultaneous Refinement with HO
NMR relaxation refinement,input of experimental data: Input of the Experimental
NMR relaxation refinement,optimal correlation time: Grid Search for Optimal
NMR relaxation refinement,quality assessment: Assessing the Quality of
NMR structure determination: NMR Structure Determination
NMR structure determination, topologies and parameters: Files “parallhdg.dna" and “topallhdg.dna"
NMR structure determination,acceptance of refined structures: Acceptance of Refined NMR
NMR structure determination,average structure: Average Structure and Rmsds
NMR structure determination,enantiomer selection: Test for the Correct
NMR structure determination,rms differences: Average Structure and Rmsds | Pairwise Rmsds
NMR structure determination,simulated annealing: Ab Initio SA Starting | Random Simulated Annealing | Simulated Annealing Refinement
NMR structure determination,substructure distance geometry: Distance Geometry
NMR structure determination,template coordinate set: Template Structure
NMR structure determination,time averaging: Time-Average Refinement
NMR structure refinement, topologies and parameters: Files “parallhdg.dna" and “topallhdg.dna"
NMR, relaxation matrix refinement: NMR Back-calculation Refinement
NOE: Distance Restraints
NOE back-calculation: NMR Back-calculation Refinement
NOE back-calculation,BPTI example: Prediction of a NOESY
NOE back-calculation,gradient expression: Analytical Expression for the
NOE back-calculation,leakage: The Relaxation Matrix
NOE back-calculation,unresolved chemical shifts: Syntax
NOE distances, restraints: Distance Restraints
NOE distances,ambiguous: Expressing ambiguous restraints using
NOE distances,averaging methods: Choice of Averaging
NOE distances,distance restraints file: Setup of Distance Restraints
NOE distances,pseudoatoms: Pseudoatoms
NOE distances,restraining functions: Choice of Restraining Functions
NOE, 3D: 3D NOE-NOE Example
NOE,time-average: Refinement Using Time-Averaged Distance
non-crystallographic symmetry: Non-crystallographic Symmetry
non-crystallographic symmetry,Bricogne conventions: Strict NCS
non-crystallographic symmetry,restrained: Non-crystallographic Symmetry
non-crystallographic symmetry,restraints: NCS Restraints
non-crystallographic symmetry,skew frame: Strict NCS
non-crystallographic symmetry,strictly identical: Non-crystallographic Symmetry | Strict NCS
nonbonded distances: Analysis of the Nonbonded
nonbonded energy terms: Nonbonded Energy Terms | Analysis of the Nonbonded
nonbonded energy terms,truncation: Nonbonded Energy Terms
nonbonded interaction, 1-4: Syntax | Syntax | Syntax | Syntax | Files “parhcsdx.pro" and “tophcsdx.pro" | Intramolecular Interactions
nonbonded parameters: Syntax
nucleic acids,molecular structure: A Nucleic Acid Structure
nucleic acids,topologies and parameters: CHARMM “top_all22*" and “par_all22*" | CHARMM “toph11.dna" and “param11.dna" | Files “topnah1e.dna" and “parnah1e.dna" | Files “parallhdg.dna" and “topallhdg.dna"
numerical precision: Set Statement
occupancy refinement: Grouped B-Factor and Occupancy
one-bond coupling restraints: One-Bond Coupling Restraints
ONEBond-statement: Syntax
ORIEnt-statement: Syntax
orthogonalized coordinates: Examples | Orthogonalization Convention
packing function: Crystallographic Target Functions | A Packing Function
paramagnetic cross-correlation rate restraint: Paramagnetic Cross-Correlation Rate Restraint
paramagnetic orientation restraint: Paramagnetic Orientation Restraint
paramagnetic pseudocontact shift restraint: Paramagnetic Pseudocontact Shift Restraint
paramagnetic relaxation enhancement, distance calculation: Distance Calculation from Paramagnetic
paramagnetic relaxation enhancement, restraints: Paramagnetic Relaxation Enhancement Restraints
paramagnetic residual dipolar coupling restraints: Paramagnetic Residual Dipolar Coupling
parameter and topology files: Topology and Parameter Files
parameter and topology files, lipids: CHARMM “top_all22*" and “par_all22*"
parameter and topology files, water: Files “toph19.sol" and “param19.sol"
parameter and topology files,carbohydrates: Files “toph3.cho" and “param3.cho"
parameter and topology files,chromophores: Files “toph19.chromo" and “param19.chromo"
parameter and topology files,crystallographic refinement: Files “parhcsdx.pro" and “tophcsdx.pro"
parameter and topology files,nucleic acids: CHARMM “top_all22*" and “par_all22*" | CHARMM “toph11.dna" and “param11.dna" | Files “topnah1e.dna" and “parnah1e.dna" | Files “parallhdg.dna" and “topallhdg.dna"
parameter and topology files,proteins: CHARMM “top_all22*" and “par_all22*" | CHARMM “toph19.pro" and “param19.pro" | AMBER/OPLS “tophopls.pro", “parhopls.pro" Files | Files “parhcsdx.pro" and “tophcsdx.pro" | Files “parallhdg.pro" and “topallhdg.pro"
parameter,writing: Writing a Parameter File
parameters: Parameter Statement
parameters, atom-based: Parameter Statement | Examples of Atom-based Modifications
parameters, hydrogen-bonding: Syntax
parameters, nonbonded: Syntax
parameters, type-based: Parameter Statement
parameters,learning: no title | Learning Atom-based Parameters
parameters,reducing: Reducing to Type-based Parameters
parsing: X-PLOR Language
partial energy terms: Symbols
PATCh statement: Topology Statement
Patterson correlation () refinement: Molecular Replacement
PCSA restraint: Pseudo Chemical Shift Anisotropy
PCSA-statement: Syntax
PDB format: Syntax
phase difference: Syntax of the Xrefin
phase restraints: Crystallographic Target Functions
pick energy: Syntax of the Pick
pick geometry: Syntax of the Pick
planarity: Conformational Energy Terms
PMAG-statement: Syntax
Powell minimization: Conjugate Gradient Minimization
print energy: Syntax of the Print
print geometry: Syntax of the Print
proteins,molecular structure: A Standard Protein Structure
proteins,topologies and parameters: CHARMM “top_all22*" and “par_all22*" | CHARMM “toph19.pro" and “param19.pro" | AMBER/OPLS “tophopls.pro", “parhopls.pro" Files | Files “parhcsdx.pro" and “tophcsdx.pro" | Files “parallhdg.pro" and “topallhdg.pro"
proton chemical shift: Proton Chemical Shift Restraints
PROTonshifts statement: Syntax
pseudo chemical shift anisotropy restraint: Pseudo Chemical Shift Anisotropy
pseudoatoms: Pseudoatoms | Pseudoatoms | NMR Structure Determination
quanta: Binary Trajectory Files
QUANTA trajectory format: Binary Trajectory Files
quaternions: 3 $\times$ 3 Matrices | Initialization
R value: Crystallographic Target Functions | Check of Data and
R value, distribution: Syntax of the Xrefin
R value,free value: Cross-validation: The Free
R value,Luzzati plot: Luzzati Plot
R value,NMR structure: Assessing the Quality of | Calculation of Different
radius of gyration: Syntax | Scaling
radius of gyration restraint: Radius of Gyration Restraints
Ramachandran plot: Ramachandran Plot
RAMAchandran-statement: Syntax
random-number function: Syntax
random-number seed: Set Statement
RDC tensor axis atoms: Requirements
RDCs: Residual Dipolar Couplings
reading,coordinates: Coordinate Statement
reading,distance restraints: Setup of Distance Restraints
reading,molecular structure: Structure Statement
reading,trajectory: Reading Trajectories
reducing parameters: Reducing to Type-based Parameters
reflection files: Reflection Files | Example: A Crystallographic Reflection
reflection files,merging files: Example: Merging Crystallographic Reflection
reflections,manipulation: Manipulating Reflection Data
reflections,writing: Syntax
relaxation energy term: The $E_{relaxation}$ Energy Term
relaxation matrix: The Relaxation Matrix
relaxation matrix refinement, NMR: NMR Back-calculation Refinement
remarks: Control Statements
repel energy term: Nonbonded Energy Terms
residual dipolar couplings: Residual Dipolar Couplings
residue-residue positional restraints, database: Residue-Residue Position/Orientation Database Restraint
residues: Syntax
restraints, dihedral angle: Dihedral Angle Restraints
restraints, harmonic plane: Plane Restraints
restraints, harmonic point: Point Restraints
restraints,coordinate: Coordinate Restraints
restraints,dihedral: Dihedral Angle Restraints
restraints,distance: Distance Restraints
restraints,distance symmetry: Distance Symmetry Restraints
restraints,harmonic coordinate: Harmonic Coordinate Restraints
restraints,planarity: Planarity Restraints
rigid-body minimization: Rigid-Body Minimization
rigid-body molecular dynamics: Rigid-Body Coordinate Space
rigid-body refinement: Rigid-Body Refinement
ring pucker: Syntax of the Pick | Syntax of the Pick
ring pucker,nucleic acids: CHARMM “toph11.dna" and “param11.dna"
rms deviation: Syntax
rmsd: Rms Differences between Coordinates | Average Structure and Rmsds | Pairwise Rmsds
rotation function,list file: The Rotation Function Listing
rotation function,output file: The Rotation Function Output
rotation matrix (3 $\times$ 3): 3 $\times$ 3 Matrices
rotation search: Rotation Search
SANI statement: Syntax - SANI
scalar j-coupling: Scalar J-Coupling Restraints
scaling of diffraction data: Crystallographic Target Functions | Syntax
segment statement: Topology Statement
selection: Atom Selection
SHAKE: Fixing Distances
simulated annealing,ab initio from template: Ab Initio SA Starting
simulated annealing,crystallographic refinement: Crystallographic Refinement by Simulated
simulated annealing,NMR refinement: Simulated Annealing Refinement
simulated annealing,preparation: Crystallographic Refinement by Simulated
simulated annealing,random coordinates: Random Simulated Annealing
simulated annealing,slow-cooling: Example: Run a Slow-cooling | Crystallographic Refinement by Simulated | Simulated Annealing Refinement
slow-cooling molecular dynamics: Example: Run a Slow-cooling
slow-cooling,crystallographic refinement: Crystallographic Refinement by Simulated
solvation: Example: Solvation of a
solvent boundary forces: Deformable Boundary Forces
solvent mask: Bulk Solvent Mask | Example: Use of a
solvent screening: Electrostatic Function
special positions: Special Positions
structure factor,normalized: Crystallographic Target Functions
structure factor,partial: Crystallographic Target Functions | Partial Structure Factors
structure factor,solvent: Example: Use of a
structure factors: Crystallographic Target Functions
structure generation,nucleic acid: A Nucleic Acid Structure
structure generation,protein: A Standard Protein Structure
structure generation,protein,with cofactor or substrate: A Protein Structure with
structure generation,protein,with metal cluster: A Protein Structure with
structure generation,protein,with water or ligands: A Protein Structure with
structure generation,viruses or multimers: Virus Structures or Structures
structure,generation: Generating the Molecular Structure
surface statement: Accessible Surface Area
symbols: Symbols
symmetry interactions,crystallographic: Crystallographic Symmetry Interactions
symmetry interactions,non-crystallographic: Non-crystallographic Symmetry Interactions
symmetry operators: Crystallographic Symmetry Interactions | Syntax | Crystallographic Target Functions | Strict NCS
symmetry,distance restraints: Distance Symmetry Restraints
tag: Syntax | Conformation vs. Residue Number
TENSOr statement: Syntax - TENSOr
time-averaged distance restraints: Refinement Using Time-Averaged Distance
topology: Topology Statement
trajectory statement: Trajectory Statement
trajectory,analysis: Analysis of Trajectories
trajectory,analysis,angular distribution: Angular Distribution Functions
trajectory,analysis,average: Average Coordinates and Fluctuations
trajectory,analysis,covariance: Covariance Analysis
trajectory,analysis,density: Density Analysis
trajectory,analysis,pick properties: Picking Properties for Trajectories
trajectory,analysis,power spectrum: Power Spectrum Analysis
trajectory,analysis,radial distribution function: Radial Distribution Functions
trajectory,analysis,time correlation: Time Correlation Analysis
trajectory,error messages: Diagnostic Error Messages
trajectory,merging coordinate files: Example
trajectory,merging files: Merging Trajectories
trajectory,reading: Reading Trajectories
trajectory,writing: Writing Trajectories
translation function,output file: The Translation Function Output
translation function,peak list: The Translation Function Listing
translation search: Translation Search
type-based parameters: Parameter Statement
unit cell constants: Crystallographic Symmetry Interactions
unknown coordinates: What to Do about
Van der Waals radii, parameters: Van der Waals radii
van der Waals radius: Van der Waals Function
van der Waals radius, in NMR protocols: NMR Structure Determination
VEANgle statement: Syntax- VEANngle
vector: Vector Statement
vectors (3d): Three-dimensional Vectors
Verlet method: Finite Difference Approximation
viruses,molecular structure: Virus Structures or Structures
water: Example: Water Molecules | Example: Solvation of a
water hydrogens: Building Hydrogen Positions
water,topologies and parameters: Files “toph19.sol" and “param19.sol"
while: Control Statements
wildcards: Wildcards
Wilson plot: Syntax of the Xrefin | Wilson Plot
writing,coordinates: Write Coordinate Statement
writing,molecular structure: Writing a Molecular Structure
writing,reflections: Syntax
writing,trajectory: Writing Trajectories
X-PLOR,input: X-PLOR Language
X-PLOR,notation: Notation
XANGle-statement: Syntax
XCCR-statement: Syntax
XDIPolar statement: Syntax - XDIPolar or
XPCS-statement: Syntax
XRDCoupling-statement: Syntax
XT1D-statement: Syntax

Xplor-NIH 2023-11-10