X-PLOR

Index

A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z

A

absolute scale

structure factors, scattering factors, 20

ambiguous restraints, 5, 27

Ambiguous Restraints for Iterative Assignment. See ARIA.

ANALYse-restraints, 31

andersen parameter, 15

Andersen thermal coupling, 4, 14

ARIA, 27

commands, 31

ASCIi, 9

Berendsen thermal coupling, 14

Brookhaven Protein Data Bank. See PDB.

bulk solvent refinement, 3

CALIbrate, 34

calibrate.xplor file, 30

calib.inp file, 30

command block

dynamic torsion, 8, 9

velocity verlet, 15

convergence

MAD phasing, 19

co-ordinate errors, 2

COUNt-violations, 33

cross-validation

MAD phasing, 19

with ensemble averaging, 5

CSEL, 9

cycles (refinement), 18

¹³C13 carbon chemical shift, 35

data conversion, 24

direct coupling constant refinement, 35

direct rotation function, 3

direct secondary carbon chemical shift refinement, 36

direct ¹H chemical shift refinement, 37

DO, 34

electron density maps, 2

example scripts, 44

errset.xplor file, 30

file.list file, 30

FIX GROUp, 8

FIX TORSion, 8

FOMs, 24

FREE BOND, 9

FREE TORSion, 8

Gaussian quadrature, 39

heavy atom

directions not fixed, 23

Hendrickson-Lattman coefficients, 23, 12

ILBFrq, 9

initialize.xplor file, 29, 31

J-coupling

NMR refinement, 35

KDIHmax, 9

lack of closure. See LOCs.

LOC

guidelines for interpreting, 23

LOCs

MAD phasing

log file

MAD phasing, compressing, 19

macrocycles, 18

MAD phasing, 2, 15

cautions, 23

LOCs, 18

sequence of jobs, 16

tutorial, 17

mad_refine.fp, 21

mad_refine.hkl, 22

mad_refine.inp

output files, 21

mad_refine.pdb, 22

mad_refine.summary, 23

MATD keyword, 40

matrix doubling, 39

MAXBond, 9

MAXChain, 9

MAXDihe, 9

maximum likelihood targets, 4, 11

MAXJoint, 9

MAXLength, 9

MAXTree, 9

mbins parameter, 13

merge.inp file, 30

MLF1 (amplitude based target), 12

MLF2 (intensity based target), 12

MLHL (target using Hendrickson-Lattman phase probability coefficients), 12

molecular replacement

multiple molecules, 2

nequ parameter, 15

NOE distance restraints

averaging, 4

NOE intensities

in refinement, 39

NOE intensity refinement, 6

non-anomalous structure factor

phases, 23

NPRInt, 10

NSAVC, 10

NSAVV, 10

NSTEp, 9

OFFSet, 10

ORIGin, 10

parameter block

xrefin, 12

parameters

refinement and phasing, 20

PDB deposition script, 3

phased translation function, 3

project.xplor file, 29, 31

proton

NMR refinement, 35

RBUF, 10

read_data_xplor file, 29

REASsign, 10

reducing data sets, 23

refinement, 5

defaults, 12

RESET

topology, 9

_A weighting, 2

sa_tad_all.inp script, 27

sa_tad_stein.inp script, 27

SCALe, 10

scripts

analyze crystallographic data, 44

ARIA method examples, 49

create parameter files for ligands, 42

distance geometry, simulated annealing, 49

electron density maps, 44

for PDB deposition, 44

generate structure and co-ordinate files, 42

geometric and energetic analysis of proteins, 42

macromolecular structure refinement, 47

MAD phasing, 43

multiconformer refinement, 49

Patterson searches and refinement, 45

pick water peaks, 45

reflection data conversion, 43

relaxation matrix refinement, 50

select reflections, 44

torsion angle dynamics, 45

¹H and ¹³C chemical shift, J-coupling refinement, 51

setup_swap.xplor file, 30

siga parameter, 13

spectra_ass.list file, 31

structure factor amplitude, 12

target keyword, 12

TBATh, 10

tcoupling option, 15

test set, 24

TIMEstep, 10

topology

specifying, 8

torsion angle dynamics, 1, 5, 7

for NMR structure determination, 26

TRAJectory, 10

VASCii, 10

VELOcity, 10

VOFFset, 10

VSCALe, 10

VSEL, 10

water picking, 3

X-PLOR

directories, 41

running, 41

X-PLOR

reflection data format, 24

X-PLOR data format, 4

X-PLOR 3.851

new features since, 1

X-PLOR 98.0

new features for crystal structure determination, 1

new features for NMR structure determination, 4

xplor_data_convert program, 24