Index
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
R
S
T
U
V
W
X
Y
Z
Index
A
- A Axis, B Axis, C Axis
- Xfit Contours menu, 497
- Abort
- Xheavy menu, 507
- Access_Surf command
- ProStat pulldown, 415
- Add 90 to Phase (Bijvoet Fourier)
- Xmergephs menu, 515
- Add_NCS_Information option, 331
- Adman, E. T., 324
- Agarwal, R. C., 323
- Alternate solid and dashed contour
- Xcontur View menu, 429
- Ammon, H. L., 325
- Anderson, W. F., 325
- Angle
- Xfit menu, 467
- Xfit View menu, 483
- Angle Weight x 10
- Xfit Refine menu, 492
- angles
- polar and Eulerian, defined, 14
- Angstroms/cm parameter
- Xcontur View menu, 428
- anomalous scatterers, 58, 62, 64
- Append
- Xfit Load Dictionary menu, 475
- Append to Solution File
- Xhercules menu, 512
- Apply
- Xcontur View menu, 429
- Xheavy Edit menu, 509
- Xheavy menu, 507
- Xprepfin menu, 521
- Xprolsqtool Reflection Limits menu, 525
- Apply Fit
- Xfit menu, 469
- Apply_Density_Mask command, 378
- Apply_Transform command
- Mol_Replacement pulldown, 372
- approximate spacing in angstroms
- Xfft menu, 437
- Arnold, E., 323
- as Group #
- Xfit Model menu, 501
- As Number, 473
- Xfit Files menu, 474
- Athay, R., 323
- Atom
- Xheavy Edit menu, 509
- Xpatpred menu, 518
- Atom Filter
- Xfit View menu, 483
- Atoms in Selected Residue
- Xfit Model menu, 498
- Auto Center
- Xcontur View menu, 429
- Auto Contour on Scroll
- Xfit Contours menu, 497
- Auto FFT after calculation
- Xfit SFCalc menu, 502, 503
- AutoFit
- Xfit LSQ Fit menu, 481
- Autonumber
- Xfit Model menu, 501
- Auto_Density_Mask command
- Modify_Density pulldown, 374
- Average over Non-Crystallographic Symmetry
- Xfit Contours menu, 497
- Average_NCS_Density command
- Modify_Density pulldown, 388
- axes
- Fourier map in Xcontur, 424
- horizontal in Xcontur, 424
- sectioning in Xcontur, 424
- vertical in Xcontur, 424
B
- B
- Xheavy Edit menu, 509
- Xpatpred menu, 518
- Babinet bulk solvent scattering correction, 43, 102, 103
- Back Clip
- Xfit menu, 466
- Badger, J., 323
- Blinking
- Xfit Show menu, 486
- Blinking Rate
- Xfit Control menu, 494
- Blow, D. M., 323, 325
- bond file
- vu format, 426
- Bond Weight x 10
- Xfit Refine menu, 492
- Bonds
- Xfit menu, 468
- bonds
- adjusting line width in Xcontur, 429
- displaying in Xcontur, 429
- Bonds File
- Xcontur Main menu, 426
- bonds, number of, in Xcontur, 426
- Box Size
- Xfit Ridgelines menu, 477
- Break Bond
- Xfit menu, 468
- Bricogne, G., 323
- Brünger, A. T., 323, 324
- Bulk solvent scattering, 43
- B-Value Plot
- Xfit View menu, 485
- B_Factor_Refine command
- Refinement pulldown, 405
C
- Calculate
- Xfft menu, 438
- Calculate All and Scale
- Xfit SFCalc menu, 502
- Calculate torsion angle for top 4 on stack
- Xfit Torsion menu, 468
- Calc_Absolute_Scatt command
- MAD pulldown, 347
- Calc_Anom_Diff command
- MAD pulldown, 341
- Calc_Fourier command
- MIR pulldown, 352
- Calc_Phases command
- MIR pulldown, 356
- C-alpha trace, comparing to structural fragments, 478
- Cancel
- Xfit menu, 469
- Canvas
- Xfit menu, 465
- canvas
- Xfit, 439
- Cell
- Xcontur Main menu, 423
- Xfit menu, 466
- Xprolsqtool menu, 522
- Center
- Xfit View menu, 482
- center
- Xfit MB3 pop-up menu, 444
- center@
- Xfit MB3 pop-up menu, 444
- Chain ID
- Xfit Model menu, 501
- Xfit View menu, 483
- Clear Contacts
- Xfit Clear Labels menu
- clearing distance/contact, 467
- Xfit Show menu, 486
- Clear Labels
- Xfit Clear Labels menu, 467
- Xfit menu, 467
- Xfit Show menu, 486
- Clear Labels and Contacts
- Xfit Clear Labels menu, 467
- Clear Selections
- Xfit Model menu, 500
- Clear Stack
- Xfit menu
- Xfit
clear stack, 467
- Close
- Xprolsqtool Reflection Limits menu, 525
.cmb file, 60- CNX, 286
- data files, 56
- simulated annealing, 100
- Coefficients
- Xfit FFT menu, 489
- coefficients
- selecting in Xfft, 435
- Col Max
- Xcontur Main menu, 424
- Col Min
- Xcontur, 424
- Coller, E., 325
- Color
- Xfit Ridgelines menu, 477
- Color Bkgnd 1
- Xfit Colors menu, 488
- Color Bkgnd 2
- Xfit Colors menu, 488
- Color Current 1
- Xfit Colors menu, 488
- Color Current 2
- Xfit Colors menu, 488
- Color Model
- Xfit Colors menu, 487
- Color Side Chain
- Xfit Ridgelines menu, 478
- Color Style
- Xfit Colors menu, 487
- Color Symm Atoms
- Xfit Colors menu, 488
- Color Vu
- Xfit Colors menu, 487
- Coloring
- Xfit View menu, 484
- Colors
- Xfit menu, 465
- Colors menu
- Xfit, 481
colors.dat file, 93- Column Origin
- Xcontur View menu, 429
- Column Ticks
- Xcontur View menu, 428
- Columns
- Xcontur Main menu, 424
- Combine_MAD_Data command
- MAD pulldown, 337
- commands
- documentation format, 3
- entering on command line in Insight, 3
- CONEXN, 111
- Constraints
- Xfit Refine menu, 491
- Contact Radius
- Xfit Control menu, 495
- Contacts command
- Symmetry pulldown, 418
- Contour
- Xfit menu, 469
- contour
- Xfit MB3 pop-up menu, 445
- Contour All Maps
- Xfit Contour menu, 469
- Contour at Center
- Xfit Contour menu, 470
- Contour Current Selection
- Xfit Contour menu, 470
- Contour Levels
- Xcontur Main menu, 424
- contour maps, 356
- Contouring Method
- Xfit Contours menu, 496
- Contours
- Xfit menu, 465
- Contours menu (Xfit), 495
- Contour_Map command
- MIR pulldown, 356
- Contour_Map_3D command
- MIR pulldown, 352
- Control
- Xfit menu, 465
- Control menu (Xfit), 492
- Corr Map File
- Xhercules menu, 511
- cross-difference Fourier maps, 10
- cross-locked rotation function, 22
- cross-rotation function, 75
- Crowther, R. A., 324
- Crystal
- Utilities pulldown, 331
- Xcontur Main menu, 423
- Xfft menu, 435
- Xfit menu, 466
- Xmerge menu, 513
- Xpatpred menu, 516
- Xprepfin menu, 519
- Xprolsqtool menu, 522
- Xresflt, 544
- Xrspace, 542
- Xskel, 545
- Xstat, 547
- crystal
- creating and editing, 331
- defining, 330
- deleting, 331
- file in Xsight, 51
- file in Xsight, creating, 53
- crystal file
- in Xcontur, 423
- crystal symmetry
- visualizing, 113
- $CRYSTALDATA, 52
- CRYSTALDATA environment variable, 331
- crystals
- database file, 52
- crystals file, 330
- Crystal_Delete option, 331
- Crystal_Directory, 331
- Cube/Sphere Radius
- Xfit Contours menu, 496
- CX Canvas (SUN only)
- Xfit menu, 465
- cycles of refinement, 525
D
- d max
- Xfit SFCalc menu, 502
- d min
- Xfit SFCalc menu, 502
- Data Are
- Xprepfin menu, 520
- Data File
- Xheavy Edit menu, 508
- Data_Control pulldown, 334
- Data_Processing command
- Data_Control pulldown, 336
- Defaults
- Xfft menu, 435
- Xprolsqtool menu, 523
- Xprolsqtool Reflection Limits menu, 525
- Xskel, 545
- Defaults menu
- Xcontur, 427
- Xfft, 438
- Delete
- Xcontur Labels menu, 430
- Xfit menu, 467
- Xheavy Edit menu, 509
- Xheavy menu, 507
- Xpatpred menu, 518
- Delete Res
- Xfit Model menu, 500
- Density
- Xfit menu, 469
- density
- fluctuations in solvent, 38
- modifying, 378
- density fitting, 391, 439
- tutorial, 193
- density flattening, 91
- density map
- contouring, 356
- density modification, 36, 81
- tutorial, 171
- Density_Fitting
- Model_Building pulldown, 391
- Density_Operation menu
- Display_Density command, 332
- Depth cue
- Xcontur, 429
- DepthCue (% front)
- Xfit Control menu, 494
- Deriv vu number
- Xfit SFCalc menu, 502, 503
- Derivative File
- Xheavy menu, 506
- Derivatives
- Xheavy menu, 506
- Derivatives of Current Atoms
- Xfit SFCalc menu, 502, 503
- Determine_Phases command
- MAD pulldown, 345
- Dictionary
- Refinement pulldown, 410
- Xfit Files menu, 475
- dictionary
- stereochemical, 110, 294
- difference Patterson function, 8
- difference Patterson maps
- PostScript output, 68
- visualizing, 67
- difference Patterson, calculating, 66
- dihedral angles
- peptide-protein, 414
- Direction of Planes
- Xfft menu, 435
- Directory
- Xcontur File menu, 425
- Xedh Files menu, 432
- Xfft menu, 435
- Xfit Files menu, 472
- Xheavy menu, 506
- Xhercules menu, 511
- Xmerge menu, 513
- Xmergephs menu, 515
- Xpatpred menu, 516
- Xprepfin menu, 519
- Xprolsqtool menu, 523
- Xresflt, 544
- Xrspace, 542
- Xskel, 545
- Xstat, 547
- Display Data
- Xrspace, 542
- Display Type
- Xcontur View menu, 428
- Display_Density command
- Utilities pulldown, 332
- Display_Recip_Space command
- Data_Control pulldown, 336
- Distance
- Xfit menu, 467
- Distances
- Xfit Refine menu, 492
- Draw
- Xcontur Main menu, 424
- Xrspace, 543
- Draw Arrows
- Xfit LSQ Fit menu, 480
- Draw Bonds
- Xcontur View menu, 429
- Draw Contacts
- Xfit Control menu, 495
- Draw Distances
- Xfit Control menu, 494
- Draw Grid of Lines
- Xcontur View menu, 429
- Draw Jack at Label Position
- Xcontur View menu, 429
- Draw Labels
- Xcontur View menu, 429
- Draw Mode
- Xfit Control menu, 493
- Draw Side by Side Stereo
- Xcontur View menu, 429
E
- Edit menu
- Xheavy, 507, 508
- Edit Script
- Xfit View menu, 482
- Edit_Density_Mask command
- Modify_Density pulldown, 375
- Eisenberg, D., 325
- electron density
- averaging by non-crystallographic symmetry, 40
- calculating with Xfft, 431
- correlation translation function, 34
- 2D contouring, 356
- Electron Density Histogram window
- Xedh, 431
- electron density map
- calculating, tutorial, 193
- examining with Xfit, 91
- generating skeleton, 544
- iso-value surfaces, 495
- viewing with Xfit, 92
- End at Residue
- Xfit Refine menu, 491
- Engh-Huber parameters, 101, 102
- Engh, R. A., 324
- envelope, protein sub-unit, 88
- Erickson, J. W., 324
- Errors
- Xfit Refine menu, 492
- Euler angles, 73
- Expand Top 2
- Xfit menu, 467
- Extend Blob Around Current Atoms by
- Xfit Contours menu, 497
F
- fast Fourier transform, 352
- fast rotation function
- invoking, 79
- Fenderson, F. F., 324
- FFT
- Xfit menu, 465
- FFT menu (Xfit), 488
- figure-of-merit, 13
- File
- Xfit View menu, 482
- Xrspace, 542
- File Filter
- Xfit Files menu, 472
- File pop-up menu
- Xcontur, 422
- File Type
- Xheavy Edit menu, 508
- Xstat, 548
- Filename
- Xfit Model menu, 498
- Files
- Xfit menu, 464
- files
- importing, exporting, reformatting, 519
- merging with Xmerge, 512
- Files menu
- Xedh, 431
- Xfit, 471
- Files Type Filter
- Xfit View menu, 484
- Filter
- Xcontur File menu, 425
- Xedh Files menu, 432
- Xresflt, 544
- .fin, 519
- Fin File
- Xhercules menu, 511
- Fin file format, 55
- Fin File to Phase
- Xmergephs menu, 515
- Fin File 1
- Xmerge menu, 513
- Fin File 2
- Xmerge menu, 513
- Find_Heavy_Atoms command
- MIR pulldown, 354
- Fine, R. M., 325
- First Files
- View menu, 483
- Fisher, R. G., 325
- Fit
- Xfit menu, 468
- Fit Model #
- Xfit menu, 468
- Fit Source Residues
- Xfit LSQ Fit menu, 480
- Fitzgerald, P. M. D., 324
- Floating menu bar
- Xfit, 442
- Fobs File
- Xprolsqtool menu, 523
- Fourier map
- contour levels, 424
- contouring of, 421
- convert to grid file, 332
- cross-difference, 352
- generating with Xfft, 431
- print sections, 427
- resizing in Xcontur, 424
- sectioning along axes, 435
- specifying in Xcontur, 425
- Fourier maps, cross-difference, 10
- fractional coordinates
- Fourier map, 422
- free R value, 43
- Front Clip
- Xfit menu, 466
- Fujinaga, M., 324
- Furey, W., 324
G
- Gelatt, C. D., Jr., 324
- Generate Symmetry Atoms
- Xfit Symm Atoms menu, 469
- geometry refinement, 488
- Get View
- Xfit View menu, 482
- GLRF program, 72
- keywords, 549-581
- storage limits, 581
- tutorial, 237
- Graph It
- Xstat, 548
- grid
- in Xcontur, 429
- Grid Number in X, Y, Z
- Xfft menu, 437
- GRINCH
- file type in Xfit, 464
- Gros, P., 324
- Group Selected Residues
- Xfit Model menu, 501
H
- H Mode
- Xfit Files menu, 474
- Hahn, T., 324
- Harding, M. M., 325
- Harker sections, 67
- Hartsuck, J. A., 325
- Heat
- Xfit Refine menu, 492
- heavy atom sites, 8-11, 68
- finding, 354
- refinement, 11, 71
- heavy atoms
- determining position with Xhercules, 509
- Help facility (Insight II), 4
- Hendrickson, W. A., 324, 325
- Herriott, J. R., 324
- Hide H's
- Xfit View menu, 483
- Histogram
- Xedh Files menu, 433
- histogram
- displaying in Xedh, 431
- histogram matching, 40, 83, 374, 378, 427
- histograms
- comparing in Xedh, 434
- generating electron-density, 427
- number of in Xedh, 433
- save as graph in Xedh, 433
- saving in Xedh, 433
- Huber-Engh stereochemical dictionary, 108
- Huber, R., 324
I
- Import_Data command
- Data_Control pulldown, 334
- Include
- Xfit View menu, 484
- Input File
- Xprepfin menu, 519
- Xresflt, 544
- Xstat, 547
- Input Format
- Xprepfin menu, 520
- Input PDB
- Xfit Files menu, 473
- Input Phase File
- Xfft menu, 435
- Xskel, 545
- Insert
- Xcontur Labels menu, 430
- Xheavy Edit menu, 509
- Xpatpred menu, 518
- Insert Res
- Xfit Model menu, 498
- Insight
- results from Xfit, 391
- IR, 5, 6
- isomorphous replacement, 5, 6, 65
- tutorial, 120
J
- jack
- Xcontur, 429
- Jeffrey. B. A., 323
- Jih, J.-H., 325
K
- K (scale factor), 42
- Kabsch, W., 324
- Karplus, M., 323
- Kim, S.-H., 325
- Kirkpatrick, S., 324
- Kraulis, P. J., 324
- Krukowski, A., 324
- Kuriyan, J., 323
L
- Label
- Xcontur Labels menu, 429
- Xheavy Edit menu, 509
- Xpatpred menu, 517
- label
- adding in Xcontur, 430
- deleting from Xcontur, 430
- replacing in Xcontur, 430
- Label Picked Atoms
- Xfit Control menu, 494
- Labels
- controlling display in Xcontur, 429
- Xcontur Labels menu, 429
- Xfit menu, 466
- labels
- controlling size in Xcontur, 429
- editing in Xcontur, 429
- Labels File
- Xcontur File menu, 425
- Labels menu (Xfit), 501
- Labels pop-up menu
- Xcontur, 427
- large term
- fast rotation function, 17
- slow rotation function, 15
- Last Files
- Xfit View menu, 483
- Lattman, E. E., 324
- Least Squares Fit
- Xfit LSQ Fit menu, 480
- least-squares minimization, 44, 107
- tutorial, 287
- Lee, B., 325
- Length of Match
- Xfit LSQ Fit menu, 480
- Lengthen Color from Picked Edge
- Xfit Ridgelines menu, 478
- Level
- Xrspace, 542
- Levinthal, C., 325
- ligand
- dictionary, 410
- ligands
- from dictionary, 110
- Limit 1
- Xresflt, 544
- Limit 2
- Xresflt, 544
- line width
- as depth cue in Xcontur, 429
- lines
- contour style in Xcontur, 429
- List
- Xcontur File menu, 425
- Xedh Files menu, 432
- Xfit Files menu, 472
- Load
- Xedh Files menu, 433
- Xfit Files menu, 476
- Load and center
- Xfit Load Model menu, 473
- Load and center if first model
- Xfit Load Model menu, 473
- Load Defaults Set
- Xprolsqtool menu, 523
- Load Derivative
- Xheavy menu, 506
- Load Dictionary
- Xfit Files menu, 475
- Load from xfft.defaults
- Xfft Defaults menu, 438
- Load Fsfour Format Map (*.map)
- Xfit Map File menu, 472
- Load Labels
- Xcontur File menu, 425
- Load Map
- Xcontur File menu, 425
- Load Model
- Xfit Files menu, 473
- Load Phases, Do Not Scale, and FFT (*.phs)
- Xfit Map File menu, 472
- Load Phases, Scale, and FFT (*.phs)
- Xfit Map File menu, 472
- Load Solution
- Xpatpred menu, 517
- Load Vu
- Xfit Files menu, 474
- Load with no centering
- Xfit Load Model menu, 473
- Load xcontur.defaults
- Xcontur Defaults menu, 430
- locked cross-rotation function, 20
- locked rotation function, 78
- locked self-rotation function, 18
- loops
- conformation refinement, 49
- model building considerations, 46
- Monte Carlo generation, 47
- random tweak generation, 46
- LSQ Fit
- Xfit menu, 465
- LSQ Fit menu
- Xfit, 478
M
- MAD, 5, 6, 57
- anomalous scattering differences, 341
- calculating scatter, 347
- combine data sets, 337
- phase determination, 345
- refine atomic model, 349
- MAD pulldown, 337
- MADSYS, 8, 11, 12
- required measurements, 59
- tutorial, 147
- MADSYS program
- keywords, 610
- program flow, 609
- Main, P., 326
- Make Ridgelines
- Xskel, 546
- Make Script
- Xfit View menu, 483
- Make Vu
- Xfit View menu, 484
- Make Vu Object from Model #
- Xfit View menu, 483
- Map
- loading into Xcontur, 422
- Xfit FFT menu, 489
- map
- contouring, 80
- in Xedh, 432
- mini, 421
- Map bounds in fraction of unit cell x 100
- Xskel, 546
- Map File
- Xcontur File menu, 425
- Xedh Files menu, 432
- Xfit Files menu, 472
- map fitting
- de novo, tutorial, 206
- Map Type
- Xfft menu, 435
- Xskel, 546
- Map Weight x 10
- Xfit Refine menu, 492
- Map #
- Xfit Contours menu, 496
- Xfit Refine menu, 490
- Xfit SFCalc menu, 502
- Maps
- Xfit Show menu, 486
- mask
- automatically generating, 374
- editing, 375
- unique protein sub-unit, 380
- Master Fin File
- Xheavy menu, 506
- Match Atom Types
- Xfit LSQ Fit menu, 480
- Matrix
- Xfit View menu, 482
- Matthews, B. W., 325
- Max
- Xfit Contours menu, 497
- Max B
- Xfit View menu, 485
- Max Resolution
- Xfit FFT menu, 489
- Maximum Density
- Xskel, 546
- maximum likelihood target, 41, 286
- McRee, D., 325
- Merge
- Xmergephs menu, 515
- merge .fin data sets, 65
- Merge_Data command
- MIR pulldown, 352
- Merge_Molecule command
- Symmetry pulldown, 420
- Merge_Phases command
- MIR pulldown, 356
- merging
- data sets, 352
- phase angles and structure factors, 356
- merging data, 512
- Method
- Xfit SFCalc menu, 502, 503
- Xheavy menu, 507
- Min Resolution
- Xfit FFT menu, 489
- mini maps, 356
- minimization, 398
- least squares, 410
- ProLSQ95, 410
- Minimize command
- Refinement pulldown, 410
- Minimum Density (rms=50)
- Xskel, 546
- Minimum Fobs to include
- Xprolsqtool Reflection Limits menu, 524
- Minimum Fobs/Sigma Ratio
- Xprolsqtool Reflection Limits menu, 525
- MIR, 5
- heavy atom refinement, 356
- merging data sets, 352
- phase refinement, 356
- scaling data sets, 352
- MIR phase calculation, 505
- MIR pulldown, 352
- Model
- Xfit menu, 466
- model
- currently active, defining in Xfit, 495
- model fitting, 92, 439
- Model menu (Xfit), 495
- Model Pick
- Xfit Control menu, 494
- model structure solution, 81
- Models
- Xfit Show menu, 486
- Model_Building pulldown, 390
- Modify_Density pulldown, 374, 378
- molecular replacement, 72, 219, 357
- molecules
- combining into single file, 420
- Molecule_Update command
- Model_Building pulldown, 391
- Mol_Replacement pulldown, 357
- Monte Carlo
- driver for simulated annealing, 49
- loop refinement, 49
- mouse behavior
- dragging speed, 461
- Mouse Damping
- Xfit Control menu, 493
- MR_Tools command
- Mol_Replacement pulldown, 373
- multiple isomorphous replacement, 5
- Multiple Wavelength Anomalous Diffraction (MAD), 57
- Multi_Body_Refine command
- Refinement pulldown, 403
N
- Name
- Xfit Model menu, 500
- Navaza, J., 325
.ncs file, 87- neighbor molecule
- generating contacts, 418
- New
- Xheavy menu, 507
- non-crystallographic symmetry
- averaging, 90
- averaging densities, 85, 374, 388
- non-crystallographic symmetry matrices, refining, 91
- non-crystallographic symmetry operations, 86
- Non_Cryst_Symmetry command
- Modify_Density pulldown, 380
- Number
- Xedh Files menu, 433
- Number of Bins
- Xmerge menu, 514
- Number of bins
- Xstat, 548
- Number of Bonds
- Xcontur Main menu, 426
- Number of Cycles
- Xfit Refine menu, 492
- NX, NY, NZ
- Xcontur Main menu, 424
- nx, ny, nz
- Xfit FFT menu, 489
O
- Occupancy
- Xheavy Edit menu, 509
- Xpatpred menu, 518
- Occupancy of Search Atom
- Xhercules menu, 512
- Offset of Vertical Axis
- Xrspace, 543
- Omit Current Atoms
- Xfit SFCalc menu, 502
- ordinary cross-rotation function, 18
- tutorial, 237
- ordinary self-rotation function, 17
- Origin
- Xcontur plot, 428
- Xpatpred menu, 518
- Other Formats
- Xprepfin menu, 520
- Outlier Filter
- Xfft menu, 436
- Output
- Xheavy menu, 506
- Xmerge menu, 513
- Output File
- Xmerge menu, 513
- Xprepfin menu, 521
- Xresflt, 544
- Output Format
- Xprepfin menu, 521
- Output Map File
- Xfft menu, 438
- Output PDB
- Xfit Files menu, 473
- Output Phase File
- Xmergephs menu, 515
- Output Phases
- Xheavy menu, 506
- Output Type
- Xmerge menu, 513
P
- Packing command
- Symmetry pulldown, 415
- Pahler, A., 325
- parameters
- customizing defaults in Xcontur, 427
- customizing defaults in Xfft, 438
- Patterson
- prediction of, 356
- prediction of peaks, 516
- Patterson calculation
- input file description, 436
- Patterson correlation refinement, 79
- Patterson correlation translation function, 32
- Patterson function, 8-11
- Patterson function map
- calculating with Xfft, 431
- Patterson maps, difference, 352
- Patterson peaks
- predicting, 356
- predicting with Xpatpred, 516
- Patterson volume, 68
- Patterson, difference, calculating, 66
- PDB File
- Xprolsqtool menu, 523
- Percent Data to Reserve for free R
- Xprolsqtool Reflection Limits menu, 524
- percentage of minimum resolution
- Xfft menu, 437
- Phase, 5
- phase combination, 514
- phase determination, 5, 63, 71
- MADSYS, 8
- preparation for model building, 63
- processes, 7
- scaling data sets, 7
- tutorial, 147
- phase determination, MAD, 6
- Phase File
- Xmergephs menu, 515
- Phase file format, 55
- Phase File Type
- Xfft menu, 436
- phase probability distribution, 12
- phase problem, 5
- Phase Type
- Xheavy Edit menu, 508
- phasing file
- producing with Xmergephs, 514
- PhiPsi Plot
- Xfit View menu, 484
- phi-psi plot
- generating, 484
- Pick Mode
- Xfit Ridgelines menu, 478
- Plan View
- Xfit View menu, 483
- Plane
- Xcontur Main menu, 424
- Plane Weight x 10
- Xfit Refine menu, 492
- Planes
- Xcontur Main menu, 424
- Planes of
- Xrspace, 542
- Plot
- Xfit Files menu, 475
- Xfit menu, 465
- Plot to PostScript File
- Xfit Plot menu, 476
- Plot to PostScript Printer
- Xfit Plot menu, 476
- Plotter (file)
- Xfit Files menu, 475
- Polar angles, 73
- PostScript
- files from Xfit, 94
- viewing files, 332
- PostScript Preview Canvas
- Xfit menu, 465
- Prediction File
- Xpatpred menu, 517
- Predict_Patterson command
- MIR pulldown, 356
- Priestle, J. P., 325
- Print
- Xcontur Print menu, 427
- Xrspace, 543
- Print File
- Xcontur Print menu, 427
- Print pop-up menu
- Xcontur, 426
- Print to
- Xcontur Print menu, 427
- PrintEach Plane Separately
- Xcontur Print menu, 427
- Printer
- Xcontur Print menu, 427
- project
- creating, 54
- creating or selecting, 331
- defining, 330
- deleting, 332
- management, 330
- starting new, 54
- working directory in Xsight, 51
- working on existing, 54
- Project command
- Utilities pulldown, 331
- projects
- database file, 52
- projects file, 330
- Project_Delete option, 332
- ProLSQ, 107
- ProLSQ interface, 522
- ProLSQ95, 44, 107
- using Xprolsqtool, 521
- Properties
- Xfit Plot menu, 475
- ProStat, 112
- ProStat pulldown, 414
- protein
- generating copies using crystallographic symmetry, 415
- relating to crystallographic symmetry, 415
- secondary structure classification, 415
- unique sub-unit mask, 380
- protein distribution, 44
- protein mask
- determining, 81
- editing, 82
- protein phases, calculation of, 12
- protein sub-unit envelope, 88
R
- R factor, 28
- Ramachandran plot, 484
- Rao, S. N., 325
- Read
- Xrspace, 542
- Read Phase File
- Xfft menu, 437
- real space refinement, 488
- real space rotation function, 23
- reciprocal space
- display of, 336
- displaying, 336
- reciprocal space viewer, 541
- Reduce Indices
- Xprepfin menu, 520
- Refine
- Xfit menu
- Xfit
refinement, 465
- Xfit Refine menu, 491
- Refine Against Map
- Xfit Refine menu, 491
- Refine menu, 488
- Refine while fitting
- Xfit Refine menu, 491
- refinement
- atomic temperature factors, 405
- minimize, 410
- multi-domain rigid body, 403
- prolsqtool, 410
- rigid-body with ROTLSQ, 408
- refinement calculations, 102
- Refinement Parameters
- Geometry Restraints menu (Xprolsqtool), 529
- Monte Carlo and Sec Str menu (Xprolsqtool), 538
- Non-Bonded Contacts menu (Xprolsqtool), 532
- Non-Crystallographic menu (Xprolsqtool), 536
- Refinement Strategy menu (Xprolsqtool), 527
- Shifts Restraints menu (Xprolsqtool), 531
- Thermal (B-Values) menu (Xprolsqtool), 534
- View Prolsq Log File menu (Xprolsqtool), 540
- View Protin Log File menu (Xprolsqtool), 540
- Xprolsqtool menu, 523
- Refinement Parameters menu
- Xprolsqtool, 525
- Refinement pulldown, 395
- Refine_Anom_Sites command
- MAD pulldown, 349
- reflection data
- convert to Fin or Phase, 56
- file formats, 54-??
- Reflection data weighting
- Xprolsqtool Reflection Limits menu, 525
- Reflection Limits
- Xprolsqtool menu, 523
- Reflection Limits menu
- Xprolsqtool, 524
- reflections
- analysis of, 414
- Relative Weight of Iso to Ano
- Xheavy Edit menu, 508
- Remington, S. J., 325
- Remove Symmetry Atoms
- Xfit Symm Atoms menu, 469
- Rename
- Xfit Contours menu, 496
- Rename Res
- Xfit Model menu, 500
- Replace
- Xcontur Labels menu, 430
- Xfit Load Dictionary menu, 475
- Xheavy Edit menu, 509
- Xpatpred menu, 518
- replacement, isomorphous, 5, 6
- Reset
- Xfit menu, 469
- Xheavy Edit menu, 509
- Xprolsqtool Reflection Limits menu, 525
- Reset to startup
- Xcontur Defaults menu, 430
- Reset to Startup values
- Xfft Defaults menu, 438
- Residues
- Xfit Model menu, 498
- Residue_Dihedral command
- ProStat pulldown, 414
- Resize
- Xcontur Main menu, 424
- Resolution
- Xheavy Edit menu, 508
- Xrspace, 542
- Xskel, 546
- Resolution Filter
- Xfft menu, 436
- resolution filter, 543
- Resolution Limit
- Xresflt, 544
- Resolution Limits
- Xprolsqtool Reflection Limits menu, 524
- Resolution Limits in Angstroms
- Xhercules menu, 511
- Reynolds, R. A., 325
- Richards, F. M., 325
- Ridge Lines File
- Xskel, 545
- Ridgeline Level
- Xfit Ridgelines menu, 477
- Ridgelines
- Xfit Files menu, 476
- Xfit menu, 464
- ridgelines
- coloring structural features, 463, 478
- generating, 391
- Ridgelines menu
- Xfit, 471
- rigid-body refinement, 104
- multiple proteins, 106
- multiple proteins, tutorial, 267
- Rigid_Body_Refine command
- Refinement pulldown, 408
- Rocking
- Xfit Control menu, 494
- Rocking Range
- Xfit Control menu, 494
- Rocking Rate
- Xfit Control menu, 494
- Rossman and Blow
- transposed matrix, 360
- Rossmann, M. B., 325
- Rossmann, M. G., 323, 325, 326
- Rotamer Search
- Xfit Refine menu, 490
- rotate
- Xfit MB3 pop-up menu, 444
- rotation function, 13
- applying solution, 372
- cross-locked, 22
- fast, invoking, 79
- general strategy, 20
- GLRF program, 72
- locked, 78
- real space, 23
- refining solutions, 79
- selecting, 358
- slow, 14, 16
- triple, 23
- visualizing results, 80
- rotation function, cross, 75
- locked, 20
- ordinary, 18
- rotation function, self, 72
- locked, 18
- ordinary, 17
- tutorial, 220
- rotation matrix
- generating, 373
- Rotational Search
- Xfit Refine menu, 490
- Rotation_Func command
- Mol_Replacement pulldown, 358
- ROTLSQ
- rigid-body refinement, 408
- RotLSQ
- rigid-body refinement, 104
- Row Max
- Xcontur Main menu, 424
- Row Min
- Xcontur Main menu, 424
- Row Origin
- Xcontur View menu, 428
- Row Ticks
- Xcontur View menu, 428
- Rows
- Xcontur Main menu, 424
- Run number
- Xprolsqtool menu, 523
- Rupley, J. A., 325
S
- Sander, C., 324
- SAVE
- Xfit menu, 470
- Save
- Xfit Files menu, 476
- Save All Vu Objects
- Xfit Save Vu menu, 474
- Save Contours as Vu file (*.vu)
- Xfit Map File menu, 473
- Save Defaults Set
- Xprolsqtool menu, 523
- Save Density as AVS Field file (*.fld)
- Xfit Map File menu, 472
- Save Derivative
- Xheavy menu, 506
- Save Graph
- Xedh Files menu, 433
- Save Histogram
- Xedh Files menu, 433
- Save Labels
- Xcontur File menu, 426
- Save Model
- Xfit Files menu, 473
- Save PDB and Bonds
- Xfit SAVE menu, 470
- Xfit Save Model menu, 474
- Save PDB File
- Xfit SAVE menu, 470
- Xfit Save Model menu, 473
- Save Phases (*.phs)
- Xfit Map File menu, 472
- save set
- label, 470
- Save Single Vu
- Xfit Save Vu menu, 474
- Save Solution
- Xpatpred menu, 517
- Save to xfft.defaults
- Xfft Defaults menu, 438
- Save Vu
- Xfit Files menu, 474
- Save xcontur.defaults
- Xcontur Defaults menu, 430
- SA_Refine command
- Refinement pulldown, 398
- Scale
- Xfit LSQ Fit menu, 480
- Xmerge menu, 514
- Scale Angstroms/cm
- Xcontur View menu, 429
- Scale Arrows x 100
- Xfit SFCalc menu, 502, 503
- scale factor (K), 42
- scaling
- data sets, 352
- scaling data sets, 7
- Scaling Type
- Xmerge menu, 514
- Scan Data
- Xprolsqtool Reflection Limits menu, 525
- scatterers, anomalous, 5, 8-11
- refinement, 11
- scattering, anomalous. See anomalous scatterers, 58
- scattering, expected, 58
- scattering, multiwavelength anamolous, 5
- Search for Top Hit
- Xhercules menu, 512
- Search Grid in Angstroms
- Xhercules menu, 511
- Search_Model command
- Mol_Replacement pulldown, 357
- SecondaryClassify command
- ProStat pulldown, 415
- SecondaryRender command
- Molecule pulldown, residue table as input, 415
- sectioning map
- Xcontur, 424
- Select Save Set
- Xfit menu, 470
- self-rotation function, 72
- calculating, tutorial, 220
- Separation
- Xfit View menu, 483
- Set Blink Group 1
- Xfit Show menu, 486
- Set Blink Group 2
- Xfit Show menu, 486
- Set to Current Color Level
- Xfit Contours menu, 497
- Set Up Refinement Residues
- Xfit Refine menu, 491
- Set View
- Xfit View menu, 482
- Setup_XPLOR command
- Refinement pulldown, 395
- Set_Subunit_Mask command
- Modify_Density pulldown, 384
- SFCalc
- Xfit menu, 466
- Xfit SFCalc menu, 502
- SFCalc menu (Xfit), 495
- Shake to reduce phase bias
- Xfit SFCalc menu, 502, 503
- Shenkin, P. S., 325
- Show
- Xfit menu, 465
- Xfit Ridgelines menu, 477
- Show menu
- Xfit, 481
- Show Torsions of Current Residue
- Xfit Torsion menu, 468
- Shrake, A., 325
- Sigma
- Xfit Refine menu, 492
- Sigma Cutoff
- Xmerge menu, 513
- Sign of Delta
- Xfit SFCalc menu, 502, 503
- simulated annealing, 43, 100, 398
- tutorial, 276
- single isomorphous replacement, 5
- SIR, 5
- Site List Scroll Window
- Xpatpred menu, 517
- Sites
- Xheavy Edit menu, 508
- Size
- Xcontur View menu, 429
- Size (of jack)
- Xcontur View menu, 429
- skeleton
- generating with Xskel, 544
- skeletonization, 391
- Skeletonization command
- Model_Building pulldown, 391
- Slab
- Xcontur, 424
- Xfit menu, 466
- Xrspace, 542
- slow rotation function, 14, 16
- Solution File
- Xhercules menu, 511
- Xpatpred menu, 517
- solvent accessible surface, 415
- Solvent Correction
- Xprolsqtool Reflection Limits menu, 525
- solvent distribution, 44
- solvent flattening, 83, 374, 378
- algorithms, 38
- Solvent Mask
- Xedh Files menu, 432
- Source-Model
- Xfit LSQ Fit menu, 479
- space groups, 331
- Split Stereo
- Xfit View menu, 483
- Spot size
- Xrspace, 542
- Stack
- Xfit menu, 467
- Start at Residue
- Xfit Refine menu, 491
- Start Refinement
- Xprolsqtool menu, 523
- statistics
- generating from reflection files, 546
- Statistics command
- MIR pulldown, 357
- ProStat pulldown, 414
- stereo
- selecting in Xcontur, 429
- separation in Xcontur, 429
- setting depth in Xcontur, 429
- Stereo Depth
- Xcontur View menu, 429
- Stereo Separation
- Xcontur View menu, 429
- stereochemical dictionary, 410
- stereochemistry
- checking with ProStat, 112
- structure factor data
- converting, 334
- importing, 334
- structure factors
- calculated from atomic model, 357
- calculating, 30
- calculating for cross-rotation function, 74
- calculating, tutorial, 232
- phase relationships, 35
- statistics, 414
- Struct_Check command
- ProStat pulldown, 414
- Styles
- Xfit Contours menu, 497
- subsets
- secondary structure, creating for Insight II, 415
- Surface
- Xfit menu, 468
- Swap
- Xfit menu, 470
- Swap f1 and f2 (isomorphous Fourier)
- Xmergephs menu, 515
- Switch F1 an F2
- Xprepfin menu, 520
- Symm
- Xrspace, 542
- Symm Atoms
- Xfit menu, 469
- Symm radius
- Xfit Control menu, 494
- symmetry
- rotation function, 373
- symmetry axis
- locating, 25
- Symmetry pulldown, 415
T
- Target-Model
- Xfit LSQ Fit menu, 480
- Ten Eyck, L. T., 325
- Terwilliger, T. C., 325
- TF program, 72
- keywords, 583-607
- storage limits, 607
- tutorial, 232, 243
- tickmarks
- axes, Xcontur, 428
- Title
- Xcontur View menu, 428
- Xfit FFT menu, 489
- Tollin, P., 325
- Tong, L., 326
- Top Hit
- Xhercules menu, 512
- Torsion
- Xfit menu, 467
- torsion
- Xfit MB3 pop-up menu, 445
- Torsion Search
- Xfit Refine menu, 491
- translate
- Xfit MB3 pop-up menu, 444
- translation function, 21, 28, 77, 367
- applying solution, 372
- electron density correlation, 34
- Patterson correlation, 32
- TF program, 72
- Translational Search
- Xfit Refine menu, 490
- Translation_Func command
- Mol_Replacement pulldown, 367
- triple rotation function. See cross-locked rotation function, 23
- Type
- Xfit Model menu, 501
- Xrspace, 542
U
- Undo Color
- Xfit Ridgelines menu, 478
- Undo Last Fit
- Xfit LSQ Fit menu, 481
- Unit Cell
- Xfft, 435
- Xheavy menu, 506
- Xmerge menu, 513
- Xresflt, 544
- Xrspace, 542
- Xskel, 545
- unit cell
- Xcontur, 423
- Update Current Atoms
- Xfit SFCalc menu, 502, 503
- Update R-density while fitting
- Xfit Refine menu, 491
- Use Data
- Xprepfin menu, 520
- Use Line Width for Depth Cue
- Xcontur View menu, 429
- Utilities pulldown, 330
- Crystal, 331
- Display_Density, 332
- Project, 331
- View_PostScript, 332
V
- van der Waals surface, 468
- van Gunsteren, W. F., 324
- Vecchi, M. P., 324
- Verbose output
- Xfit Refine menu, 492
- View
- Xfit menu, 465
- View CorrelationMap
- Xhercules menu, 511
- View menu
- Xfit, 481
- View pop-up menu
- Xcontur, 427
- View_PostScript command
- Utilities pulldown, 332
- Vu File
- Xfit Files menu, 474
- vu format
- methods for producing, 426
- Vu number
- Xfit View menu, 484
- Vu Objects
- Xfit Show menu, 486
W
- Wang, B. C., 326
- Wang, H., 325
- water
- difference map, 97
- finding, 392
- fitting in maps, 96
- locating automatically, 97
- locating automatically, tutorial, 299
- Waters command
- Model_Building pulldown, 392
- Weaver, L. H., 325
- Weight
- Xheavy Edit menu, 508
- what to graph
- Xstat, 548
- Width
- Xcontur View menu, 429
- Williams, T. V., 326
- Write Prediction
- Xpatpred menu, 517
X
- x
- Xcontur Labels menu, 430
- Xcontur
- accessing, 356
- alternating contour line style, 429
- bonds file, specifying, 426
- Defaults menu, 427
- deleting label, 430
- description, 421
- drawing bonds, 429
- drawing grid, 429
- editing label, 429
- file path, specifying, 425
- File pop-up menu, 422
- jack, 429
- labels file, loading, 425
- labels file, saving, 426
- labels file, specifying, 425
- labels, editing, 429
- line widths for bonds, 429
- loading a file, 425
- loading default parameters, 430
- main menu, 422
- new label, 430
- plot, centering, 429
- postscript file of map, 426
- print or postscript, specifying, 427
- printing map, 426
- replacing label, 430
- resetting default parameters, 430
- saving default parameters, 430
- scaling the plot, 429
- stereo depth, 429
- stereo images, 429
- stereo separation, 429
- view, modifying
- Xcontur
view, defaults, 427
- Xcontur Labels pop-up menu, 427
- x-coordinate
- Xcontur label, 430
- Xedh
- changing directory, 432
- description, 427
- Electron Density Histogram window, 431
- identification of histograms, 434
- map file, 432
- reading solvent mask, 432
- save histogram as graph, 433
- saving histogram, 433
- specifying histogram, 433
- specifying number of histograms, 433
- Xfft, 8
- accessing, 352
- Defaults menu, 438
- description, 431
- filtering reflections, Patterson, 436
- grid size vs. resolution, 437
- grid spacing in angstroms, 437
- input file, 435
- load defaults, 438
- loading default parameters, 435
- naming output file, 438
- phase file type, 436
- read phase file, 437
- resetting default parameters, 438
- resolution filter, 436
- saving defaults, 438
- sectioning along axes, 435
- selecting coefficients, 435
- setting grid, 437
- Xfit, 91, 92
- A Axis, B Axis, C Axis, 497
- accessing pop-up menus, 440
- activating objects, 468
- Angle Weight x 10, 492
- Angle (View menu), 483
- as Group #, 501
- Atom Filter, 483
- atom labels, clearing, 467
- atom labels, modifying, 466
- atoms
- picking in Xfit, 466
- picking/rotating in Xfit, 440
- Atoms in Selected Residue, 498
- Auto Contour on Scroll, 497
- Auto FFT after calculation, 502, 503
- AutoFit, 481
- Autonumber, 501
- Average over Non-Crystallographic Symmetry, 497
- Blinking, 486
- blinking object, 465
- Blinking Rate, 494
- bond two atoms, 468
- Bond Weight x 10, 492
- bones, 464
- break bond, 468
- B-Value Plot, 485
- Calculate All and Scale, 502
- calculate angles, 467
- calculate distance, 467
- canvas, 439
- Center, 482
- center mode, MB2, 444
- center translation, 440
- centering atoms, 444
- Chain ID, 483
- Chain ID (Model menu), 501
- changing contour colors, 497
- Clear Contacts, 486
- Clear Labels, 486
- clear labels/contacts, 467
- clear labels/distances, 467
- Clear Selections, 500
- clipping z axis, 466
- Coefficients (FFT menu), 489
- Color Bkgnd 1, 488
- Color Bkgnd 2, 488
- Color Current 1, 488
- Color Current 2, 488
- Color Model, 487
- Color Side Chain, 478
- Color structural features, 477
- Color Style, 487
- Color Symm Atoms, 488
- Color Vu, 487
- Coloring (View menu), 484
- colors, 93, 465
- Colors menu, 481
- colors, defaults for atoms, 481
- Constraints (Refine menu), 491
- Contact Radius, 495
- contour at center, 470
- contour center, 445
- Contour menu, 469
- contouring, 469
- Contouring Method, 496
- Contours menu, 465, 495
- Control menu, 492
- Cube/Sphere Radius, 496
- d max (SFCalc menu), 502
- d min (SFCalc menu), 502
- Delete Res, 500
- deleting atom from stack, 467
- DepthCue (% front), 494
- Deriv vu number, 502, 503
- Derivatives of Current Atoms, 502, 503
- description, 439
- dictionary, loading, 475
- display range, 466
- display ridgeline object, 477
- displaying objects, 465
- distance aid, 442
- Distance (Refine menu), 492
- Draw Arrows, 480
- Draw Contacts, 495
- Draw Distances, 494
- Draw Mode, 493
- Edit Script, 482
- End at Residue, 491
- Errors (Refine menu), 492
- expert menu, 447
- Extend Blob Around Current Atoms by, 497
- fast/PostScript display, 465
- file types, 464
- File (View menu), 482
- Filename, 498
- Files menu, 471
- Files Type Filter, 484
- filtering files, 472
- First Files, 483
- Fit Source Residues, 480
- fit/unfit model toggle, 470
- floating menu bar, 442
- Get View, 482
- grid control, 465
- Group Selected Residues, 501
- Heat (Refine menu), 492
- Hide H's, 483
- hydrogen information, 474
- Include, 484
- Insert Res, 498
- inserting residues, 499
- keyboard shortcuts, 441
- Label Picked Atoms, 494
- Labels menu, 466, 501
- Last Files, 483
- Least Squares Fit, 480
- Length of Match, 480
- Lengthen Color from Picked Edge, 478
- list atoms in stack, 467
- load model, 473
- loading dictionary, 475
- loading .bones file, 476
- Make Script, 483
- Make Vu, 484
- Make Vu Object from Model #, 483
- Map Weight x 10, 492
- Map # (Contours menu), 496
- Map # (Refine menu), 490
- Map # (SFCalc menu), 502
- Map (FFT menu), 489
- Maps (Show menu), 486
- map, specifying, 472
- Match Atom Types, 480
- Matrix, 482
- Max B, 485
- Max Resolution (FFT menu), 489
- Max (Contours menu), 497
- Method (SFCalc menu), 502, 503
- Min Resolution, 489
- Model menu, 466, 495
- Model Pick, 494
- Model # (SFCalc menu), 502
- Models (Show menu), 486
- modify position, 469
- modifying labels, 501
- mouse behavior, 440
- Mouse Damping, 493
- move mode, MB2, 444
- Name (Model menu), 500
- Number of Cycles (Refine menu), 492
- nx, ny, nz (FFT menu), 489
- Omit Current Atoms, 502
- omit maps, 502
- overview, 439
- panning/zooming, 440
- PDB file, saving, 473
- pentamers, 499
- PhiPsi Plot, 484
- pick mode, 478
- picking atoms, 466
- picking/rotating atoms, 440
- pinning pop-up menu, 440
- Plan View, 483
- Plane Weight x 10, 492
- Plot menu, 475
- plot parameters, 465
- plotting, 94
- pop-up menu, default, 443
- PostScript plot files, 94
- PostScript preview, 465
- PostScript, generating, 475
- quits without saving, 464
- reading files, 471
- Refine Against Map, 491
- Refine while fitting, 491
- Refine (Refine menu), 491
- refinement, 488
- Rename, 496
- Rename Res, 500
- Residues, 498
- restore position, 469
- results into Insight, 391
- ridgeline density, adjusting, 477
- ridgelines, 464
- Ridgelines menu, 471
- Rocking, 494
- Rocking Range, 494
- Rocking Rate, 494
- Rotamer Search (Refine menu), 490
- rotate mode, MB2, 444
- rotating canvas, 440
- Rotational Search (Refine menu), 490
- save set, selecting, 470
- saving model, 470
- saving ridgelines, 476
- Scale Arrows x 100, 502, 503
- Scale (LSQ Fit menu), 480
- script files, 481
- selecting models, 468
- Separation (View menu), 483
- Set Blink Group 1, 486
- Set Blink Group 2, 486
- Set to Current Color Level, 497
- Set Up Refinement Residues, 491
- Set View, 482
- SFCalc menu, 466, 495
- Shake to reduce phase bias, 502, 503
- Show menu, 465, 481
- Sigma (Refine menu), 492
- Sign of Delta, 502, 503
- Source-Model, 479
- specifying crystal file, 466
- specifying Fourier calculations, 465
- specifying .bones file, 476
- Split Stereo, 483
- Start at Residue, 491
- stereo, 442, 447, 463
- Styles (Contours menu), 497
- surface density, 469
- Symm radius, 494
- symmetry atoms, generate, 469
- symmetry atoms, remove, 469
- symmetry toggle, 469
- system parameters, 465
- Target-Model, 480
- Title (FFT menu), 489
- torsion mode, MB2, 445
- Torsion Search (Refine menu), 491
- torsion, calculating, 467
- translate active portion, 444
- Translational Search (Refine menu), 490
- Type (Model menu), 501
- Undo Color, 478
- Undo Last Fit, 481
- unit cell parameters, 466
- Update Current Atoms, 502, 503
- Update R-density while fitting, 491
- van der Waals surface, 468
- Verbose output (Refine menu), 492
- View menu, 465, 481
- Vu files, 474
- Vu files, saving, 474
- Vu file, saving, 474
- Vu number, 484
- Vu Objects, 486
- vu objects, 95
- Vu objects, creating, 465
- Zoom, 482
- 1, 2, 3, 4, and 5, 497
- Xfit Files menu, 473
- Xfit LSQ Fit menu, 478
- X-GEN data processing, 336
- Xheavy, 11
- Abort, 507
- accessing, 356
- Apply, 507
- Apply (Edit menu), 509
- Atom (Edit menu), 509
- B (Edit menu), 509
- Data File (Edit menu), 508
- Delete, 507
- Delete (Edit menu), 509
- Derivative File, 506
- Derivatives, 506
- description, 505
- Directory, 506
- Edit, 507
- Edit menu, 508
- Edit pop-up menu, 507
- File Type (Edit menu), 508
- Insert (Edit menu), 509
- Label (Edit menu), 509
- Load Derivative, 506
- Master Fin File, 506
- Method, 507
- New, 507
- Occupancy (Edit menu), 509
- Output, 506
- Output Phases, 506
- phase probability distribution, 12
- Phase Type (Edit menu), 508
- Relative Weight of Iso to Ano, 508
- Replace (Edit menu), 509
- Reset (Edit menu), 509
- Resolution (Edit menu), 508
- Save Derivative, 506
- Sites (Edit menu), 508
- Unit Cell, 506
- Weight (Edit menu), 508
- X, Y, Z (Edit menu), 509
- Xhercules, 9
- Append to Solution File, 512
- Corr Map File, 511
- description, 509
- Directory (main menu), 511
- Fin File (main menu), 511
- main menu, 511
- Occupancy of Search Atom, 512
- Resolution Limits in Angstroms, 511
- Search for Top Hit, 512
- Search Grid in Angstroms, 511
- Solution File (main menu), 511
- Top Hit, 512
- View CorrelationMap, 511
- X, Y, and Z Bounds in Fractionals, 511
- Xmerge, 7
- accessing, 352
- Crystal (main menu), 513
- description, 512
- Directory (main menu), 513
- Fin File 1 (main menu), 513
- Fin File 2 (main menu), 513
- Number of Bins (main menu), 514
- Output File (main menu), 513
- Output Type (main menu), 513
- Output (main menu), 513
- Scale (main menu), 514
- Scaling Type (main menu), 514
- Sigma Cutoff (main menu), 513
- Unit Cell (main menu), 513
- Xmergephs
- accessing, 356
- Add 90 to Phase (Bijvoet Fourier) (main menu), 515
- description, 514
- Directory (main menu), 515
- Fin File to Phase (main menu), 515
- Merge (main menu), 515
- Output Phase File (main menu), 515
- Phase File (main menu), 515
- Swap f1 and f2 (isomorphous Fourier) (main menu), 515
- Xpatpred
- accessing, 356
- Atom (main menu), 518
- B (main menu), 518
- confirming Xhercules results, 510
- Crystal (main menu), 516
- Delete (main menu), 518
- description, 516
- Directory (main menu), 516
- Insert (main menu), 518
- Label (main menu), 517
- Load Solution (main menu), 517
- Occupancy (main menu), 518
- Origin (main menu), 518
- Prediction File (main menu), 517
- Replace (main menu), 518
- Save Solution (main menu), 517
- Site List Scroll Window (main menu), 517
- Solution File (main menu), 517
- Write Prediction (main menu), 517
- X, Y, Z (main menu), 517
- Xpatpred menu, 516
- X-PLOR
- set-up, 395
- Xprepfin
- Apply (main menu), 521
- Crystal (main menu), 519
- Data Are (main menu), 520
- description, 519
- Directory (main menu), 519
- Input File (main menu), 519
- Input Format (main menu), 520
- Other Formats (main menu), 520
- Output File (main menu), 521
- Output Format (main menu), 521
- Reduce Indices (main menu), 520
- Switch F1 and F2 (main menu), 520
- Use Data (main menu), 520
- Xprolsqtool, 108
- accessing, 410
- Apply (Reflection Limits menu), 525
- Cell (main menu), 522
- Close (Reflection Limits menu), 525
- Crystal (main menu), 522
- Defaults (main menu), 523
- Defaults (Reflection Limits menu), 525
- description, 521
- Directory (main menu), 523
- Fobs File (main menu), 523
- Load Defaults Set (main menu), 523
- Minimum Fobs to include (Reflection Limits menu), 524
- Minimum Fobs/Sigma Ratio (Reflection Limits menu), 525
- PDB File (main menu), 523
- Percent Data to Reserve for free R (Reflection Limits menu), 524
- Refinement Parameters menu, 525
- Refinement Parameters (main menu), 523
- Refinement Parameters/Geometry Restraints menu, 529
- Refinement Parameters/Monte Carlo and Sec Str menu, 538
- Refinement Parameters/Non-Bonded Contacts menu, 532
- Refinement Parameters/Non-Crystallographic menu, 536
- Refinement Parameters/Refinement Strategy menu, 527
- Refinement Parameters/Shifts Restraints menu, 531
- Refinement Parameters/Thermal (B-Values) menu, 534
- Refinement Parameters/View Prolsq Log File menu, 540
- Refinement Parameters/View Protin Log File menu, 540
- Reflection data weighting (Reflection Limits menu), 525
- Reflection Limits menu, 524
- Reflection Limits (main menu), 523
- Reset (Reflection Limits menu), 525
- Resolution Limits (Reflection Limits menu), 524
- Run number (main menu), 523
- Save Defaults Set (main menu), 523
- Scan Data (Reflection Limits menu), 525
- Solvent Correction (Reflection Limits menu), 525
- Start Refinement (main menu), 523
- # of Reflections in input (Reflection Limits menu), 525
- # of Reflections used (Reflection Limits menu), 525
- Xresflt
- Crystal, 544
- description, 543
- Directory, 544
- Filter, 544
- Input File, 544
- Limit 1, 544
- Limit 2, 544
- Output File, 544
- Resolution Limit, 544
- Unit Cell, 544
- Xrspace
- accessing, 336
- Crystal, 542
- description, 541
- Directory, 542
- Display Data, 542
- Draw, 543
- File, 542
- Level, 542
- Offset of Vertical Axis, 543
- Planes of, 542
- Print, 543
- Read, 542
- Resolution, 542
- Slab, 542
- Spot size, 542
- Symm, 542
- Type, 542
- Unit Cell, 542
- Xsight
- setting up to run, 53
- starting up, 3
- tutorial list, 117
- Xskel
- accessing, 391
- coloring ridgelines in Xfit, 471
- Crystal, 545
- Defaults, 545
- description, 544
- Directory, 545
- Input Phase File, 545
- Make Ridgelines, 546
- Map bounds in fraction of unit cell x 100, 546
- Map Type, 546
- Maximum Density, 546
- Minimum Density (rms=50), 546
- Resolution, 546
- Ridge Lines File, 545
- Unit Cell, 545
- Xstat
- accessing, 357
- Crystal, 547
- description, 546
- Directory, 547
- File Type, 548
- Graph It, 548
- Input File, 547
- Number of bins, 548
- what to graph, 548
- Xtalview
- accessing, 391
- X, Y, and Z Bounds in Fractionals
- Xhercules menu, 511
- X, Y, Z
- Xheavy Edit menu, 509
- Xpatpred menu, 517
Y
- y
- Xcontur Labels menu, 430
- Yarmush, D. L., 325
- y-coordinate
- Xcontur label, 430
Z
- z
- Xcontur Labels menu, 430
- z-coordinate
- Xcontur label, 430
- Zhang, K. Y. D., 326
- Zoom
- Xfit View menu, 482
Symbols
- # of Reflections in input
- Xprolsqtool Reflection Limits menu, 525
- # of Reflections used
- Xprolsqtool ReflectionLimits menu, 525
- $CRYSTALDATA, 52
- least squares fitting. See also LSQ, 465
- $XTALVIEWHOME/data/colors.dat, 486
.cmb file, 60.ncs file, 87
Numerics
- 1, 2, 3, 4, and 5
- Xfit Contours menu, 497
- 3D structure
- comparing values to knowledge base, 414
Last updated January 28, 2000 at 03:50PM Pacific Standard Time.
Copyright © 2000, Molecular Simulations Inc. All rights
reserved.