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Index

, gif
( )
( )
1--4 interaction , gif , gif , gif , gif , gif
:==
<* *> , gif
< >
R value , gif
R value, distribution
R value,free R value
R value,Luzzati plot
R value,NMR structure , gif
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accessible surface area
anomalous scattering
application , gif
atom-based parameters , gif
atomic form factors
atom properties
atom selection
atom selection, fragile
atom tag , gif
B-factor refinement , gif
Backus-Naur notation
benchmark results
bond angle deviations
bond length deviations
bound smoothing
Brookhaven Protein Data Bank
building,hydrogens
carbohydrates,topologies and parameters
centroid search
CHARMM trajectory format
chiral centers
chirality , gif
chromophores,topologies and parameters
completeness of diffraction data
conformational analysis
conjugate gradient minimization
constraints,coordinate
constraints,fixing atomic positions
constraints,fixing distances
constraints,SHAKE
constraints interaction statement
control statement
coordinates
coordinates,best fit
coordinates,comparison set
coordinates, fractionalization , gif
coordinates,manipulating
coordinates, orthogonalization , gif
coordinates,rms difference
coordinates,rms difference (rmsd) analysis
coordinates,rms difference analysis
coordinates,rms difference,pairwise
coordinates,rotation and translation
coordinates, unknown
coordinates,writing
crystallographic diffraction data
crystallographic refinement
crystallographic refinement, atomic positions
crystallographic refinement, simulated annealing
crystallographic refinement, B-factors , gif
crystallographic refinement,alternate conformations,disorder
crystallographic refinement,bad contacts
crystallographic refinement,initial structure check
crystallographic refinement,linear correlation coefficient
crystallographic refinement,occupancies
crystallographic refinement,overview
crystallographic refinement,phase accuracy
crystallographic refinement,slow-cooling
crystallographic refinement,special positions
crystallographic refinement,target functions
crystallographic refinement,topologies and parameters
crystallographic refinement,weights
crystal packing
deletion of atoms
deviation from ideality
diffraction data
diffraction data, completeness
diffraction data, expanding
diffraction data, reducing
diffraction data,manipulation
diffraction data,scaling , gif
dihedral angle restraints
dimensioning of X-PLOR
display
distance geometry,van der Waals interactions
distance,between atoms
distance analysis
distance difference matrix
distance geometry , gif
distance geometry, accuracy parameter
distance geometry,bond angle constraints
distance geometry,bound smoothing
distance geometry,dihedral angle constraints
distance geometry,distance bounds
distance geometry,embedded substructures
distance geometry,embedding
distance geometry,full-structure embedding
distance geometry,improper angle constraints
distance geometry,metrization
distance geometry,pseudoatoms
distance geometry,regularization of coordinates
distance geometry,rigid group
distance geometry,SA-regularization of structures
distance geometry,scaling
distance geometry,triangle inequalities
distance matrix
distance restraints
distance restraints, restraining functions
distance restraints,averaging methods
distance restraints,disulfide bonds
distance restraints,hydrogen bonds
distance restraints,reading
distribution medium of X-PLOR
disulfide bridge
disulfide bridges
duplicating the molecular structure
electron density map
electron density map, map
electron density map,map file
electron density map,omit map
electron density map,SA-refined omit map
embedding
empirical energy function
energy,analysis
energy, bond
energy, bond angle
energy, conformational
energy,crystallographic symmetry
energy, dihedral angle
energy, electrostatic
energy, hydrogen bond
energy, improper angle
energy,interaction between selected atoms
energy,intermolecular , gif
energy,intramolecular
energy,non-crystallographic symmetry
energy, nonbonded
energy,pick
energy,print
energy,second function , gif
energy, torsion angle
energy,turning on or off
energy, van der Waals
energy analysis, conformational terms
energy analysis,nonbonded terms
energy analysis,setting the weight
energy evaluation
energy function , gif
energy minimization
equal sign
Eulerian angles
evaluate
example files,on-line
fast Fourier transformation , gif , gif
figure of merit , gif , gif
filenames
flags
for ... in
force-field
fractional coordinates
fractionalized coordinates
fragile atom selection
free R value
Friedel mates
geometric analysis , gif
geometry,pick
geometry,print
harmonic restraints
heavy-side function
help on-line
histidine protonation
hydrogen-bond donors and acceptors
hydrogen-bonding parameters
hydrogen building
hydrogens , gif
hydrogens,naming convention
if ... then
inertia tensor
installation of X-PLOR
interchain interaction energy
intramolecular interactions
Langevin dynamics , gif
Lattman's angles
learning parameters
Lee and Richards algorithm
Lennard-Jones potential , gif
letters,uppercase and lowercase
lipids,topologies and parameters
loops , gif , gif
Luzzati plot
manipulating coordinates
manipulation,diffraction data
Mathematica
matrices
Maxwellian distribution function
messages
metrix matrix distance geometry
metrization
minimization
minimization,conjugate gradient
minimization,rigid-body
mirror images
molecular dynamics
molecular dynamics,angular distribution
molecular dynamics,average displacement
molecular dynamics,covariance
molecular dynamics,density
molecular dynamics,finite difference approximation
molecular dynamics,merging files
molecular dynamics,orienting trajectory frames
molecular dynamics,pick properties
molecular dynamics,power spectrum
molecular dynamics,radial distribution function
molecular dynamics,restarts
molecular dynamics,simulation , gif , gif
molecular dynamics,slow-cooling
molecular dynamics,temperature control
molecular dynamics,temperature control,Langevin dynamics
molecular dynamics,temperature control,temperature coupling
molecular dynamics,temperature control,velocity rescaling
molecular dynamics,time correlation
molecular dynamics,trajectories
molecular dynamics,trajectory analysis
molecular dynamics,velocity assignment
molecular replacement
molecular replacement,cluster analysis
molecular replacement,cluster criteria
molecular replacement,comparing rotation matrices
molecular replacement,contour plots
molecular replacement,cross rotation function,PC-refinement , gif
molecular replacement,cross-rotation function
molecular replacement,direct rotation function
molecular replacement,elbow angle modification
molecular replacement,packing function
molecular replacement,rigid-body refinement
molecular replacement,rotation search
molecular replacement,self-rotation function
molecular replacement,translation function,asymmetric unit
molecular replacement,translation function,finding second molecule
molecular replacement,translation function,relative z position
molecular replacement,translation function,using PC-refined model
molecular replacement,translation search
molecular structure file
molecular structure,append
molecular structure,deletion
molecular structure,disulfide bridge
molecular structure,duplicating
molecular structure,examples
molecular structure,generation
molecular structure,histidine protonation
molecular structure,incomplete polypeptide chain
molecular structure,nucleic acid
molecular structure,patching , gif
molecular structure,polypeptide chain
molecular structure,protein
molecular structure,protein,unusual geometries
molecular structure,reading
molecular structure,sequence
molecular structure,solvent and solute
molecular structure,unknown atoms
molecular structure,viruses or multimers
molecular structure,water
molecular structure,writing
NCS , gif
Newton's equations of motion
NMR, relaxation matrix refinement
NMR relaxation refinement, R value
NMR relaxation refinement,against NOESY intensities
NMR relaxation refinement,cutoffs
NMR relaxation refinement,including solvent spectra
NMR relaxation refinement,input of experimental data
NMR relaxation refinement,optimal correlation time
NMR relaxation refinement,quality assessment
NMR structure determination
NMR structure determination, topologies and parameters
NMR structure determination,acceptance of refined structures
NMR structure determination,average structure
NMR structure determination,enantiomer selection
NMR structure determination,rms differences , gif
NMR structure determination,simulated annealing , gif , gif
NMR structure determination,substructure distance geometry
NMR structure determination,template coordinate set
NMR structure refinement, topologies and parameters
NOE
NOE, 3D
NOE,time-average
NOE back-calculation
NOE back-calculation,BPTI example
NOE back-calculation,gradient expression
NOE back-calculation,leakage
NOE back-calculation,unresolved chemical shifts
NOE distances, restraints
NOE distances,averaging methods
NOE distances,distance restraints file
NOE distances,pseudoatoms
NOE distances,restraining functions
non-crystallographic symmetry
non-crystallographic symmetry,Bricogne conventions
non-crystallographic symmetry,restrained
non-crystallographic symmetry,restraints
non-crystallographic symmetry,skew frame
non-crystallographic symmetry,strictly identical , gif
nonbonded distances
nonbonded energy terms , gif
nonbonded energy terms,truncation
nonbonded interaction, 1--4 , gif , gif , gif , gif , gif
nonbonded parameters
nucleic acids,molecular structure
nucleic acids,topologies and parameters , gif , gif , gif
numerical precision
occupancy refinement
orthogonalized coordinates , gif
packing function , gif
parameter,writing
parameter and topology files
parameter and topology files, lipids
parameter and topology files, water
parameter and topology files,carbohydrates
parameter and topology files,chromophores
parameter and topology files,crystallographic refinement
parameter and topology files,nucleic acids , gif , gif , gif
parameter and topology files,proteins , gif , gif , gif , gif
parameters
parameters, atom-based , gif
parameters, hydrogen-bonding
parameters,learning
parameters, nonbonded
parameters,reducing
parameters, type-based
parsing
partial energy terms
PATCh statement
Patterson correlation (PC) refinement
PDB format
phase difference
phase restraints
pick energy
pick geometry
planarity
Powell minimization
print energy
print geometry
proteins,molecular structure
proteins,topologies and parameters , gif , gif , gif , gif
pseudoatoms , gif , gif
quanta
QUANTA trajectory format
quaternions , gif
radius of gyration , gif
Ramachandran plot
random-number function
random-number seed
reading,coordinates
reading,distance restraints
reading,molecular structure
reading,trajectory
reducing parameters
reflection files , gif
reflection files,merging files
reflections,manipulation
reflections,writing
relaxation energy term
relaxation matrix
relaxation matrix refinement, NMR
remarks
repel energy term
residues
restraints,coordinate
restraints,dihedral
restraints, dihedral angle
restraints,distance
restraints,distance symmetry
restraints, harmonic plane
restraints, harmonic point
restraints,harmonic coordinate
restraints,planarity
rigid-body minimization
rigid-body molecular dynamics
rigid-body refinement
ring pucker , gif
ring pucker,nucleic acids
rmsd , gif , gif
rms deviation
rotation function,list file
rotation function,output file
rotation matrix (33)
rotation search
scaling of diffraction data , gif
segment statement
selection
SHAKE
simulated annealing, ab initio from template
simulated annealing,crystallographic refinement
simulated annealing,NMR refinement
simulated annealing,preparation
simulated annealing,random coordinates
simulated annealing,slow-cooling , gif , gif
slow-cooling,crystallographic refinement
slow-cooling molecular dynamics
solvation
solvent mask , gif
solvent screening
special positions
structure,generation
structure factor,normalized
structure factor,partial , gif
structure factor,solvent
structure factors
structure generation,nucleic acid
structure generation,protein
structure generation,protein,with cofactor or substrate
structure generation,protein,with metal cluster
structure generation,protein,with water or ligands
structure generation,viruses or multimers
surface statement
symbols
symmetry,distance restraints
symmetry interactions,crystallographic
symmetry interactions,non-crystallographic
symmetry operators , gif , gif , gif
tag , gif
time-averaged distance restraints
topology
trajectory,analysis
trajectory,analysis,angular distribution
trajectory,analysis,average
trajectory,analysis,covariance
trajectory,analysis,density
trajectory,analysis,pick properties
trajectory,analysis,power spectrum
trajectory,analysis,radial distribution function
trajectory,analysis,time correlation
trajectory,error messages
trajectory,merging coordinate files
trajectory,merging files
trajectory,reading
trajectory,writing
trajectory statement
translation function,output file
translation function,peak list
translation search
type-based parameters
unit cell constants
unknown coordinates
Van der Waals radii, parameters
van der Waals radius
van der Waals radius, in NMR protocols
vector
vectors (3d)
Verlet method
viruses,molecular structure
water , gif
water,topologies and parameters
water hydrogens
while
wildcards
Wilson plot , gif
writing,coordinates
writing,molecular structure
writing,reflections
writing,trajectory
X-PLOR,dimensioning
X-PLOR,input
X-PLOR,installation
X-PLOR,list of subdirectories
X-PLOR,notation


Sat Mar 11 09:37:37 PST 1995