Checklist of Crystallographic Functions
Included in SDP for Windows
Initialization
functions
- empirical formula processing
- cell constant calculation
- cell reduction
- symmetry generation
- molecules per cell determination
Data processing
functions
- Enraf Nonius data processing
- Siemens data processing
- Rigaku data processing
- Stoe data processing
- Mar data processing
- background correction
- scan speed correction
- peak profile analysis
- learned profile processing
- static background processing
- attenuation correction
- Lorentz polarization correction
- cell constant transfer
- space group determination
- scattering factor generation
- x-ray, neutron, electron data handling
- ion scattering modification
- monitor reflection processing
- psi scan data processing
Data analysis
functions
- intensity vs. decay calculation
- intensity vs. time graphing
- optimum psi scan determination
- psi scan averaging
- psi scan plotting
- crystal distances & angles calculation
- crystal planes & dihedral angles
- crystal drawing & real-time rotation
- Wilson plot calculation
- Debye curve calculation
- K-curve calculation
Data correction
functions
- linear decay correction
- anisotropic decay correction
- spherical absorption correction
- psi scan empirical absorption correction
- Fourier series empirical absorption correction
- numerical absorption correction
- glass capillary absorption correction
Data handling
functions
- data listing by various classes
- data sorting by various classes
- data resequencing
- data set merging & scaling
- equivalent data averaging
- standard deviation recalculation
- data redefinition by rotation axis
- data editing
- weak data elimination
- equivalent data elimination
- redundant data elimination
- Freidel pair elimination
- specific data elimination
Data weighting
functions
- non-Poisson contribution weights
- pivot point weighting
- unit weighting
- modified unit weighting
- Cruickshank polynomial weights
- modified Cruickshank polynomial
- Killean & Lawrence weighting
- Dunitz-Seiler modified weighting
- unobserved or weak data treatment
Direct methods
functions
- normalized structure amplitudes
- statistical analysis of E
- parity group rescaling of E
- N(Z) probability distribution
- sigma1 and sigma2 phase relationship calculation
- convergence mapping
- magic integer representation
- weighted tangent refinement
- statistically weighted tangent refinement
- figure of merit calculation
- Karle recycling
- MULTAN techniques
- SHELXS techniques
- RANTAN techniques
- SIR techniques
- Patterson search techniques
Fourier functions
- conventional Fourier calculation
- fast Fourier transform (FFT)
- difference Fourier calculation
- 2Fo-Fc synthesis
- weighted Fourier calculations
- Patterson function
- origin-removed Patterson
- Patterson interpretation
- E-map calculation
- peak search for positive density
- valley search for negative density
- symmetry equivalent peak rejection
- "ghost" peaks/atoms identity
- electron density error estimation
- interactive numeric map examination
- map rotation to general plane
- electron density contouring
- +/- density contour differentiation
- crater identification on contours
- atom label mark on contour maps
Atom handling
functions
- atom addition
- atom editing
- atom renaming
- atom deletion
- atom list sorting
- atom list reordering
- atom listing
- peak to atom transfer
- identification of atoms on special positions
- parameter refinement prohibition
- parameter constraint automation
- anisotropic conversion
- isotropic conversion
- riding atom definition
- coordinate rotation about axis
- coordinate transformation by matrix
- coordinate translation along axis
- assembly into asymmetric unit
- calculation of H atom positions
- regularization of methyl H atoms
- machine setting calculation for models
Least-squares
functions
- structure factor calculation
- full-matrix refinement
- refinement on F or F2
- full data refinement with unobserved data
- observed data only refinement
- sin Ø / lambda limitation capability
- scattering averaging for disorders
- anomalous dispersion correction
- atom block inclusion without refinement
- parameter restraints and resetting
- riding atom refinement
- occupancy refinement
- secondary extinction refinement
- absolute configuration refinement
- convergence testing
- matrix inversion
- correlation coefficient calculation
- interface to SHELXL-93 refinement program
Interactive
graphics functions
- display of peak numbers
- display of refined atoms
- display of bonded contacts
- display of partial unit cell
- display of single unit cell with edges
- display of multiple unit cells
- variable colors for atoms
- user defined rotation about axis
- realignment along axis
- realignment in plane
- real-time spinning of drawing
- user controlled spinning direction
- dynamic drawing magnification
- 3-D left/right stereo view drawing
- 3-D red-green stereo display
- depth cue display
- bond distance measurement
- bond angle measurement
- torsional angle measurement
- coordinate identification
- deletion of atoms from view
- undeletion of removed atoms
- add/delete of non-bonded atoms
- insertion/removal of atom labels
- insertion/removal of H atoms
- insertion/removal of H labels
- transfer coordinates to refinement
- transfer of orientation to ORTEP
- transfer of orientation to PLUTO
- transfer of orientation ProGraph
- transfer to Fourier contouring
- support for most display devices
- support for mouse
Presentation
graphics functions
- ORTEP drawing production
- PLUTO drawing production
- ProGraph drawing production
- space filling drawing
- thermal motion drawing
- ball & stick drawing
- hydrogen bonding drawing
- backbone chain drawing
- alternative drawing methods
- automatic setup of draw commands
- hidden line removal
- colored atom & bond support
- orientation transfer from
- interactive graphics
- Protein Data Bank support
- helix representation
- cylinder representation
- ß-pleated sheet representation
- secondary light source
- base plane shadow
- support for variable font sizes
- support for laser printers
- support for ink-jet color printers
- support for BMP files
- transfer of drawings within Windows
Derived results
functions
- automatic bond determination using radii
- bond connectivity search
- bond distance calculation
- bond angle calculation
- torsional angle calculation
- error estimation using variance
- error using variance/covariance
- least-squares planes calculation
- dihedral angle calculation
Statistical
analysis functions
- data collection order analysis
- magnitude of Fo analysis
- sin Ø / lambda analysis
- h,k,l index analysis
- parity group analysis
- weighting scheme analysis
- graphing of above analyzes
- extinction effects analysis
- extinction parameter estimation
- sorted listing of worst reflections
Publication
preparation functions
- automatic table preparation for:
- atomic coordinates
- isotropic or equivalent thermal parameters
- anisotropic parameter (ß's)
- general thermal parameter (U's)
- general thermal parameter (B's)
- rms amplitudes of thermal vibration
- sorted molecular distances
- sorted molecular angles
- least-squares planes
- dihedral angles
- experimental procedures
- structure solution
- structure refinement
- parenthetical insertion of esd's in all tables
- table preparation with or without H's
- text generation of experimental section in word processing form
- inclusion of Greek and math symbols
- inclusion of equations
- interface to word processor
- support for Postscript production
- CIF file preparation
Graphics slide
show functions
- selected images saved
- selected images viewed
- slide show of saved images
- Windows interface to PhotoShop
- and other graphics software
- drawings and graphs include:
- ORTEP
- PLUTO
- ProGraph
- crystal decay plot
- absorption plot
- Wilson plot
- R factor plot
- atom shift plot
- magnitude of Fo plot
- sin Ø / lambda plot
- h,k,l index analysis
- parity group analysis
- weighting scheme analysis
Communication
functions
- network link through Windows
- E-mail link through Windows
- modem link through Windows
- file conversion and reformatting
- SHELX data file import/export
- ASCII data file import/export
- ASCII atom file import/export
- PDB atom file import/export
- CIF structure archiving
- CIF structure retrieval
Menu functions
- Windows design
- Pull down menus for:
- File
- Edit
- Data
- Solve
- Atoms
- Refine
- Graphics
- Publication
- View
- Help
- parameter entry windows
- defaults for all entries
- buttons for basic operations:
- Save
- Exit
- Calculate
- Modify
- View Summary
- View Details
- Graph/Plot
- Print
- Undo
- button bar
- output windows with scrolling
- tutorial with step-by-step procedure
- Windows support for hundreds of hardware devices
Operating System
- Windows 3.1
- Windows 95/98 (recommended)
System Requirements
- 386 or higher (Pentium recommended)
- 8MB memory (16MB recommended)
- 20MB disk space (40MB recommended)
- 1.44MB diskette drive
- color monitor (15" or 17" recommended)
@ 800x600 resolution with small fonts recommended
256 colors required for ProGraph
- 2- or 3-button mouse
- CD-ROM drive (for Brookhaven Protein Data Bank only)
- modem (33.6 recommended)
- printer (Postscript laser and/or color inkjet recommended)
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Last modified: April 27, 2002