Index

,

( )

( )

1--4 interaction , , , , ,

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<* *> ,

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R value ,

R value, distribution

R value,free R value

R value,Luzzati plot

R value,NMR structure ,

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accessible surface area

anomalous scattering

application ,

atom-based parameters ,

atomic form factors

atom properties

atom selection

atom selection, fragile

atom tag ,

B-factor refinement ,

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 ,

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 ,

coordinates,manipulating

coordinates, orthogonalization ,

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 ,

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 ,

dihedral angle restraints

dimensioning of X-PLOR

display

distance geometry,van der Waals interactions

distance,between atoms

distance analysis

distance difference matrix

distance geometry ,

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 ,

energy,intramolecular

energy,non-crystallographic symmetry

energy, nonbonded

energy,pick

energy,print

energy,second function ,

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 ,

energy minimization

equal sign

Eulerian angles

evaluate

example files,on-line

fast Fourier transformation , ,

figure of merit , ,

filenames

flags

for ... in

force-field

fractional coordinates

fractionalized coordinates

fragile atom selection

free R value

Friedel mates

geometric analysis ,

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 ,

hydrogens,naming convention

if ... then

inertia tensor

installation of X-PLOR

interchain interaction energy

intramolecular interactions

Langevin dynamics ,

Lattman's angles

learning parameters

Lee and Richards algorithm

Lennard-Jones potential ,

letters,uppercase and lowercase

lipids,topologies and parameters

loops , ,

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 , ,

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 ,

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 ,

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 ,

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 ,

NMR structure determination,simulated annealing , ,

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 ,

nonbonded distances

nonbonded energy terms ,

nonbonded energy terms,truncation

nonbonded interaction, 1--4 , , , , ,

nonbonded parameters

nucleic acids,molecular structure

nucleic acids,topologies and parameters , , ,

numerical precision

occupancy refinement

orthogonalized coordinates ,

packing function ,

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 , , ,

parameter and topology files,proteins , , , ,

parameters

parameters, atom-based ,

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 , , , ,

pseudoatoms , ,

quanta

QUANTA trajectory format

quaternions ,

radius of gyration ,

Ramachandran plot

random-number function

random-number seed

reading,coordinates

reading,distance restraints

reading,molecular structure

reading,trajectory

reducing parameters

reflection files ,

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 ,

ring pucker,nucleic acids

rmsd , ,

rms deviation

rotation function,list file

rotation function,output file

rotation matrix (33)

rotation search

scaling of diffraction data ,

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 , ,

slow-cooling,crystallographic refinement

slow-cooling molecular dynamics

solvation

solvent mask ,

solvent screening

special positions

structure,generation

structure factor,normalized

structure factor,partial ,

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 , , ,

tag ,

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 ,

water,topologies and parameters

water hydrogens

while

wildcards

Wilson plot ,

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