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, 32
- ambiguous restraints, 7, 38
- Ambiguous Restraints for Iterative Assignment. See ARIA.
- ANALYse-restraints, 43
- andersen parameter, 21
- Andersen thermal coupling, 6, 20
- ARIA, 39
- commands, 43
- ASCIi, 16
B
- Berendsen thermal coupling, 20
- Brookhaven Protein Data Bank. See PDB.
- bulk solvent refinement, 4
C
- CALIbrate, 45
- calibrate.xplor file, 41
- calib.inp file, 41
- command block
- dynamic torsion, 15, 16
- velocity verlet, 21
- convergence
- MAD phasing, 31
- co-ordinate errors, 4
- COUNt-violations, 45
- cross-validation
- MAD phasing, 30
- with ensemble averaging, 7
- crystallographic data files, 69
- crystallographic map files, 72
- CSEL, 16
- cycles (refinement), 29
- 13C13 carbon chemical shift, 46
D
- data conversion, 36
- direct coupling constant refinement, 46
- direct rotation function, 5
- direct secondary carbon chemical shift refinement, 47
- direct 1H chemical shift refinement, 48
- DO, 46
E
- electron density maps, 4
- example scripts, 56
- file formats, 72
- errset.xplor file, 41
F
- file.list file, 41
- FIX GROUp, 15
- FIX TORSion, 15
- FOMs, 35
- FREE BOND, 15
- FREE TORSion, 15
G
- Gaussian quadrature, 51
- grep
- example for convergence, 31
H
- heavy atom
- directions not fixed, 35
- Hendrickson-Lattman coefficients, 35
- Hendrickson-Lattman phase probability coefficients, 18
I
- ILBFrq, 16
- initialize.xplor file, 40, 42
J
- J-coupling
- NMR refinement, 46
K
- KDIHmax, 15
L
- lack of closure. See LOCs.
- LOC
- guidelines for interpreting, 34
- LOCs
- MAD phasing
- log file
- MAD phasing, compressing, 30
M
- macrocycles, 29
- MAD phasing, 3, 27
- LOCs, 30
- sequence of jobs, 28
- tutorial, 28
- mad_refine.fp, 33
- mad_refine.hkl, 33
- mad_refine.inp
- output files, 33
- mad_refine.pdb, 34
- mad_refine.summary, 34
- MATD keyword, 51
- matrix doubling, 51
- MAXBond, 15
- MAXChain, 15
- MAXDihe, 15
- maximum likelihood targets, 6, 17
- MAXJoint, 16
- MAXLength, 15
- MAXTree, 15
- mbins parameter, 19
- merge.inp file, 41
- MLF1 (amplitude based target), 18
- MLF2 (intensity based target), 18
- MLHL (traget using Hendrickson-Lattman phase probability coefficients), 19
- molecular replacement
- multiple molecules, 4
- mp technology, 8
- MP_SET_NUMTHREADS, 9
- MSI_XPLOR_NMRLIB variable, 9
- MSI_XPLOR_NPROC, 9
- MSI_XPLOR_TEST variable, 10
- MSI_XPLOR_TOPPAR variable, 10
- MSI_XPLOR_TUTORIAL variable, 10
- MSI_XPLOR_XTALLIB variable, 10
- MSI_XPLOR_XTALMACRO variable, 10
N
- nequ parameter, 21
- 13NMR refinement, 46
- nmrlib directory, 9
- NOE distance restraints
- averaging, 6
- NOE intensities
- in refinement, 50
- NOE intensity refinement, 8
- non-anomalous structure factor
- phases, 34
- NPRInt, 16
- NSAVC, 16
- NSAVV, 16
- NSTEp, 16
O
- OFFSet, 16
- operating system
- requirements, 9
- ORIGin, 16
P
- parameter block
- xrefin, 18
- parameters
- refinement and phasing, 31
- PDB deposition script, 5
- phased translation function, 5
- processors
- single or multi, 8
- project.xplor file, 40, 42
- proton
- NMR refinement, 46
R
- RBUF, 16
- read_data_xplor file, 41
- REASsign, 16
- reducing data sets, 35
- refinement, 7
- defaults, 19
- reflection record
- example, 71
- requirements
- environment, 9
- RESET
- topology, 16
S
A weighting, 3- sa_tad_all.inp script, 38
- sa_tad_stein.inp script, 38
- SCALe, 16
- Scalepack/Denzo-to-X-PLOR program, 5
- scripts
- analyze crystallographic data, 56
- ARIA method examples, 62
- create parameter files for ligands, 54
- distance geometry, simulated annealing, 62
- electron density maps, 56
- for PDB deposition, 55
- generate structure and co-ordinate files, 53
- geometric and energetic analysis of proteins, 54
- macromolecular structure refinement, 60
- MAD phasing, 55
- multiconformer refinement, 62
- Patterson searches and refinement, 58
- pick water peaks, 58
- reflection data conversion, 54
- relaxation matrix refinement, 63
- select reflections, 56
- torsiona angle dynamics, 56
- 1H and 13C chemical shift, J-coupling refinement, 64
- setup_swap.xplor file, 42
- siga parameter, 19
- spectra_ass.list file, 42
- structure factor amplitude, 18
T
- target keyword, 18
- TBATh, 17
- tcoupling option, 22
- test directory, 10
- test set, 35
- threads
- number used, 9
- TIMEstep, 17
- topology
- specifying, 15
- torsion angle dynamics, 3, 7, 14
- for NMR structure determination, 37
- TRAJectory, 17
V
- VASCii, 17
- VELOcity, 17
- VOFFset, 17
- VSCALe, 17
- VSEL, 17
W
- water picking, 4
X
- X-PLOR
- running, 53
- X-PLOR
- reflection data format, 36, 69
- X-PLOR data format, 5
- X-PLOR 98.0
- cautions, 35
- new features for crystal structure determination, 2
- new features for NMR structure determination, 6
Last updated January 8 1999.
Copyright © 1998, 1999, Molecular Simulations Inc. All rights
reserved.