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The platon crystallographic package - səhifə 74

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Oszlanyi, G. & Suto, A. (2004) Acta Cryst., A60, 134-141,
Oszlanyi, G. & Suto, A. (2005) Acta Cryst., A61, 147-152. 
Parthe, E. & L.M.Gelato, L.M. (1984)  Acta Cryst., A40, 169-183.
Pilati, T. & Forni, A. (1998) J. Appl. Cryst., 31, 503-504 
Pilati, T. & Forni, A. (2000), J. Appl. Cryst. 33, 417.
Santoro, A. & Mighell, A.D.  (1972) Acta Cryst., A28, 284-287. 
Schomaker, V. & K.N.Trueblood, K.N. (1968). Acta Cryst., B24, 63-76.  
Sheldrick, G.M. (2008) Acta Cryst., A
Sluis, P. van der & Spek, A.L. (1990a) Acta Cryst., C46, 883-886.
Sluis, P. van der & Spek, A.L. (1990b) Acta Cryst., A46, 194-201. 
Spek, A.L. (1988) J. Appl. Cryst., 21, 578-579.
Spek, A.L. (2003) J. Appl. Cryst. 36, 7-13. 
Spek, A.L. (2009) Acta Cryst., D65, 148-155. 
Tooke, D.M. & Spek, A.L. (2005) J. Appl. Cryst. 38, 572-573.
Zimmermann, H. & Burzlaff, H. (1985) Z. fur Krist., 170, 241-246.  

INDEX – Where to Find Information on ? in this Document  


For each item listed below, references to the chapters (Ch), appendix (App) or sections (Sec) 
in this manual with relevant information on that item are given.
ABSGAUSS
Sec-1.3.5.4
ABSTOMPA
Sec-1.3.5.3
ABSSPHERE 
Sec-1.3.5.6
ABSPSI 
Sec-1.3.5.2
ADDSYM
Ch-4
ANALYSIS-of-VARIANCE
Sec-1.3.6.5
ARU'S
Sec-0.4, Sec-2.4.3
ASYM
Sec-1.3.4.8
ASYM VIEW
Sec-1.3.6.2
BERRY PSEUDO ROTATION
BIJVOET PAIR ANALYSIS
Sec-1.3.6.6
BOND VALENCE
Sec-1.3.2.14
CALC 
App-VI
CAVITY PLOT
Sec-1.3.3.8
CHARGE FLIPPING
Ch-9
CIF CREATION
Sec-1.3.7.13
CIF2SHELX
Sec-1.3.7.15
COMPARE
App-VIII
CONTOURED MAPS
Ch-7
CREMER&POPLE ANALYSIS
Sec-1.3.2.13
DIFFERENCE MAP/PEAK LIST
Sec-1.3.6.4
DELRED
Sec-1.3.4.9
EXOR
Sec-1.3.7.7
EXPAND TO P1
Sec-1.3.7.3
FLIPPER
Ch-9
GRAPHICS
HELENA
App-VII
HIRSHFELD RIGID BOND TEST
HOOFT PARAMETER 
Sec-1.3.6.6
HYDROGEN BONDS
Sec-1.3.2.7
IMPLEMENTATION 
Ch-1
LEPAGE
Sec-1.3.4.8
MOLFIT
Sec-1.3.1.9
MOLSYM
Sec-1.3.4.10
MULABS
Sec-1.3.5.1
NEWMAN PROJECTIONS
Sec-1.3.1.3
NEWSYM
Sec-1.3.4.6
NONSYM
Sec-1.3.4.7
ORTEP
Sec-1.3.1.2
PACKING INDEX
Ch-5
PATTERSON
Sec-1.3.1.13
PDB CREATION
Sec-1.3.7.14
PLANES
Sec-1.3.1.5

PLATON PACKAGE
Ch-0
PLATON TOOL
Ch-2
PLUTON 
Ch-3
POLYHEDRA
Sec-1.3.1.6
POVRAY
SIMULATED POWDER PATTERN
Sec-1.3.1.10, Sec-1.3.1.11
RADIAL DISTRIBUTION FUNCTION
Sec-1.3.1.12
RADII
App-IV
RENAME
Sec-1.3.7.9
RENUMBERING
Sec-1.3.7.10
RES CREATION
Sec-1.3.7.12
RINGS
Sec-1.3.1.4
R/S-ASSIGNMENT
SHORTCUT OPTIONS
Sec-1.1
SHXABS
Sec-1.3.5.7
SOLV
Ch-5, Sec-1.3.3.1
SPACE GROUP
App-III
SPACE GROUP FROM EXTINCTIONS
Sec-1.3.4.11
SPF FORMAT DEFINITION
A-I.1
STRAIN ANALYSIS
Sec-1.3.6.14
STRUCTURE TIDY 
Sec-1.3.6.13
SYSTEM S
Ch-10
SQUEEZE
Ch-5
TLS-RIGID BODY ANALYSIS
Sec-1.3.2.8
TWINROTMAT
Ch-6
VALIDATION
Ch-8 
VOIDS
Ch-5
XTAL HABIT
Sec-1.3.5.15

Document Outline

  • 1.1 – PLATON Tool – Command Line Invocation Shortcuts
  • 1.3.1.2 - ORTEP/ADP – Automatic Display of Displacement Parameters
  • 1.3.1.3 - Newman-Plots
  • 1.3.1.4 - Ring-Plots
  • 1.3.1.5 – Plane-Plot – Least Squares Plane Plots  
  • 1.3.1.6 - POLYHEDRA –  Plot 
  • Fig. 1.3.1.6-1 – Polyhedra plot style.
  • 1.3.1.7 – ContourDif – Contoured Difference Density Map Plot  
  • 1.3.1.8 – Contour-Fo - F(obs) MAP
  • 1.3.1.9 – AutoMol-Fit - Automatic Residue Fitting
  • Fig. 1.3.1.9-2 – Quaternion Best fit of Inverted Molecule #1 on Molecule #2.
  • Quaternion Fit of Molecules from Different Sources
  • 1.3.1.10 – HKL2Powder - Simulated Powder Pattern from HKL-Iobs
  • 1.3.1.11 – SimPowderP - Simulated Powder Pattern
  • 1.3.1.12 – RadDisFun - Simulated Radial Distribution Function
  • 1.3.1.13 – PATTERSON
    • Default instructions for PLUTON
  • 1.3.2.1 - CALC ALL
  • 1.3.2.2 - CALC INTRA
  • 1.3.2.3 - CALC INTER
  • 1.3.2.4 - CALC COORDN
  • 1.3.2.5 - CALC METAL
  • 1.3.2.6 – CALC GEOM 
  • 1.3.2.7 - H-BOND ANALYSIS
  • 1.3.2.8 – TMA & Rigid Body Analysis
    • Test Example [Data: anthracene.spf]:  Herbstein & Kaftory (1976).
  • 1.3.2.9 – L.S.-PLANE - Interactive calculation of least squares planes.
  • 1.3.2.10 – DihedAngle - Interactive calculation of dihedral angles between least squares planes.
  • 1.3.2.11 – AngleLines -Interactive calculation of angle between two lines. 
  • 1.3.2.12 - AngLsplLin - Interactive Calculation of the Angle between a Least Squares Plane and a Bond.
  • 1.3.2.13 – CremerPople - Interactive Calculation and Display of Cremer & Pople Ring-Puckering Parameters. 
  • 1.3.2.14 – Bond Valence Analysis
  • 1.3.2.15 – HFIX-RES - Generate SHELXL-Style HFIX Instructions
    • 1.3.3.1 – CALC SOLV – Determine the Solvent Accessible Volume
    • 1.3.3.2 – CALC K.P.I. – Calculate Solvent Accessible Volume + Packing Index.
  • Packing Index
  • 1.3.3.3 – SQUEEZE – Handling of Disordered Solvent in the Refinement
    • Implementation and Use:
    • The result of a SQUEEZE calculation will be in five files
    • The General SQUEEZE Keyboard Instruction:
    • Notes 
    • Interpretation of the results
  • Potential Problems and Pitfalls
  • 1.3.3.4 - CALC FCF
  • 1.3.3.5 - CONTOURED SQUEEZE MAP
  • 1.3.3.6 – SOLV-F3D
  • 1.3.3.7 - SOLV – PLOT
  • Example - Solvent Accessible Volume
  • Example - Ohashi-volume
  • 1.3.3.8 – CAVITY-PLT -A Routine for the Visualisation of Empty Spaces
  • 1.3.3.11 - FLIP MENU - Charge Flipping Menu
  • 1.3.3.12 - FLIP SHOW - Visualization of the Charge Flipping Process
  • 1.3.3.13 - FLIP PATT - Single Starting Point Charge Flipping
  • 1.3.3.14 – Flipper 25 - Multiple Starting Point Charge Flipping
  • 1.3.3.15 – STRUCTURE? - From Data to Refined Structure by Charge Flipping
  • 1.3.4.1 – ADDSYM 
  • Tool for the detection of missed or pseudo higher symmetry in data supplied in CIF, RES or SPF format. See Chapter 4 for full details and examples.
    • Fig. 1.3.4.1.-1. Example of a structure that was published in the orthorhombic space group Pbca but shown by ADDSYM to belong to the cubic space group Pa-3. The symmetry operations in white are the ones for Pbca. The additional threefold axes are presented in red. This side menu shows options to change various tolerances and to produce either a display of the averaged structure or a RES file suitable to continue refinement in the higher symmetry group. The KeepMon-I-n Toggle allows the algorithm to reain I centering and n glides when that leads to closer to 90 degrees beta angles.
    • Keyboard Instruction options:
  • 1.3.4.2 - ADDSYM  EQUAL
  • 1.3.4.3 - ADDSYM  EXACT 
  • 1.3.4.4 -  ADDSYM PLOT 
  • 1.3.4.5 - ADDSYM SHELXL
  • EXAMPLE
  • 1.3.4.7 – NONSYM - Search for and analysis of non-crystallographic symmetry 
  • 1. Intra-molecular
  • 2. Inter-molecular
    • Instructions
  • 1.3.4.8 – LEPAGE – Report Higher Lattice Symmetry with the LePage Tool 
    • Example of 'x.spf' (triclinic to cubic I)
  • 1.3.4.9 – DELRED – Report Higher Lattice Symmetry with the DELRED Tool 
    • Example of 'x.spf' (triclinic to cubic I)
  • 1.3.4.10 – MOLSYM
  • 1.3.4.11 - SPACE GROUP DETERMINATION 
  • 1.3.4.12 – ASYM – Sort & Merge Reflection Data
    • PURPOSE
  • 1.3.4.13 - ASYM FRIEDEL
  • 1.3.4.14 - LePageTwin
  • 1.3.4.15 – TwinRotMat -Determine Twin Matrix from Fo/Fc Data
    • 1.3.5.1 - MULABS - Blessing's Method for Absorption Correction 
    • Worked Example
  • 1.3.5.2 - ABSP - PSI-Scan Based Correction for Absorption
    • 1.3.5.3 - ABST - Analytical Absorption Correction  
    • Absorption Correction Test Data and Results
  • 1.3.5.4 - ABSG – Correction for Absorption with Gaussian Integration
  • 1.3.5.5 – ABSX – Crystal Dimension Optimization
  • 1.3.5.6 - ABSS - Spherical Absorption Correction 
  • 1.3.5.7 - SHXABS - Empirical Absorption Correction
  • 1.3.5.15 - XTAL HABIT – Display of a Face Indexed Crystal
    • 1.3.6.1 - Validation – Validation Tests on CIF(+FCF) & CCDC-CIF-data 
    • 1.3.6.2 – ASYM-VIEW – Inspect the Data in Diffraction Sphere Sections 
    • Example: Needed are the file asym.hkl and a file asym.ins with the following content: 
  • 1.3.6.3 - FCF-VALIDATION
  • 1.3.6.4 – DifFourier – Peak Search and Analysis of a Difference Density Map 
  • 1.3.6.5 - Analysis of Variance 
  • 1.3.6.6 - Bijvoet-Pair Analysis and Bayesian Statistics
  • Comparison of the Flack and Bayesian Statistics approach.
    • Example of a Heavy Atom Structure in P1
    • Bayesian Statistics
    • Concluding remarks
    • 1.3.6.7 – ASYM-EXPECT – Exact Expected Reflection Number  Count 
  • 1.3.6.8 – ASYM-VALIDATION
  • 1.3.6.9 - SUPPLEMENTARY MATERIAL
  • 1.3.6.10 – EXPECT-HKL – Estimate Number of expected reflections 
    • 1.3.6.11 - PLATON CSD-CELL – Search the CSD for Related Lattices 
    • 1.3.6.12 - CSD-QUEST Interface – Search the CSD for Related Structures
  • 1.3.6.13 - STRUCTURE TIDY – Standardized Inorganic Structure Data
  • 1.3.6.14 - Strain Analysis
  • 1.3.6.15 - CIF FILE GENERATION (LOCAL)
  • 1.3.7.1 – SYSTEM-S – A Guided/Automatic Structure Determination Tool
  • 1.3.7.2 - FCF2HKL – Create an HKLF4 Style File from an FCF Style File
  • 1.3.7.3 – Expand2P1 – Create an Expanded to P1 Parameter Set RES file
  • 1.3.7.4 – FCF-GENER – Create an FCF style File from Cell Content Data 
  • 1.3.7.6 – HKL-Transf - Transformation of SHELXL HKLF4 + Direction Cosines
  • 1.3.7.7 – EXOR-RES – Work-up of a Raw Structure Solution Peak List
  • 1.3.7.9 – Rename-res – Interactive Renaming of Atom labels in a RES File
  • 1.3.7.10 – Auto-Renum – Automatic Renumbering of the Atoms in a RES File
  • 1.3.7.11 – SPF-eld - Create an SPF Standard File from Input File Data
  • 1.3.7.12 – SHELXL-res – Create a RES Standard File from Input File Data
  • 1.3.7.13 – CIF-acc - Create a CIF Styled File from Input File Data
  • 1.3.7.14 – PDB-pdb – Create a PDB Styled File from Input File Data
  • 1.3.7.15 – CIF2SHELXL – Convert CIF&FCF to SHELX .ins & .hkl Input Files
  • Black-and-White Color in PLUTON
  • 2 - BWC Atom-Types
  • 3 - BWC Residue Types
  • 4 - BWC ARU-Types
    • Option 1: Global Color
    • Option 2: Per Atom Type
    • Option 3: Per Residue type
    • Option 4: Per ARU
  • Black-and-White Color in PLUTON
  • 1 - BWC Global
  • 2 - BWC Atom-Types
  • 3 - BWC Residue Types
  • 4 - BWC ARU-Types
    • Option 1:
    • Option 2:
    • Option 3:
    • Option 4:
    • Option 1:
    • Option 2:
    • Option 3:
    • Option 4:
  • Example:
    • Option 1:
    • Option 2:
    • Option 3:
    • Option 4:
  • FORMULA: The Formula instruction specifies the atom types and their number in the molecule. Along with Z it determines the unit cell content. The formula can be changed during the structure determination process. Elements can be added when needed. 
  • Z: Z should be specified such that, along with the formula, it represents the unit cell contents. 
  • PATTY:Clicking on this button invokes the DIRDIF/PATTY program suite for the structure determination of 'heavy atom' structures via Patterson techniques. 
  • ORIENT: Clicking on this button invokes the DIRDIF/ORIENT program suite for structure determination based on an orientation search with a known structural fracment (model). 
  • SHELXS86: Clicking on this button invokes a 'stripped' SHELXS86 version. A structure solution by Direct Methods (TREF) is attempted. 
  • SIR97: Clicking on this button invokes the SIR97 (Direct Methods) structure determination package. 
  • SIR2004: Clicking on this button invokes the SIR2004 (Direct Methods) structure determination package.
  • EXORS: Automatic work-up of raw model (e.g. from Direct Methods) to a more complete model with automatically assigned atom-types. The EXORS procedure is based on a sequence of displacement parameter refinements and difference maps (using SIR). 
  • EXORD: Automatic work-up of raw model (e.g. from Direct Methods) to a more complete model with automatically assigned atom-types. The EXORD procedure is based on the PHASEX procedure in DIRDIF. 
  • Features and Options
  • HDIF: Hydrogen atom position pick-up from a difference map followed by population refinement. 
  • HFIX: Introduction of hydrogen atoms via the SHELXL/HFIX mechanism. 
  • INVERT: Inversion of the Absolute Structure:
  • HFREE: Release all AFIX constraints set with HFIX. This allows for the refinement of previously fixed positional parameters. 
  • ASYM: Clicking in the left box will generate an averaged reflection set for the current symmetry with systematic extinctions removed. See ASYM for more details. 
  • VIEW:Clicking in the right box will invoke the display of the reciprocal lattice in order to inspect for data quality and completeness. See ASYM-VIEW for more details. 
  • SQUEEZE: Clicking in this box will initiate a 'SQUEEZE' calculation. 
  • FCF: Add solvent contribution to the SHELXL produce FCF to produce an FCF based on the original reflection intensities.
  • ADDSYM:Clicking on ADDSYM invokes the S-instruction 'PLATON ADDSYM'. The current 's.res' is checked for potential (missed) higher symmetry. Reported new (missed) symmetry is displayed in RED preceded by M/P. Transfer to the suggested space group can be accomplished by clicking on TRMX. The relevant alternative directories and links are setup automatically. The new (adapted) .res is copied as well. 
  • SOLV:Clicking on SOLV invokes the S-instruction 'CALC SOLV'. The current 's.res' is checked for 'solvent accessible areas', possibly indicating missed (disordered) atoms/sites. 
  • VALIDATION: Clicking in the left box invokes a CIF-Validation run in order to detect possible problems with the current analysis. 
  • REPORT: Clicking in the right box should generate a report on the current structure analysis. 
  • TREE: The TREE instruction provides a listing of all relevant files, directories and current links for the current compound. 
  • LIST: The LIST instruction gives an overview of current status and parameter values. 
  • CELL: This the first instruction in the start-up sequence of a new compound related directory tree. 
  • HELENA: The program HELENA may be invoked for the reduction of CAD4 data into a standard shelx.hkl file (including direction cosines). 
  • (to be done)
  •  
  •  
  • LIST RES: The current (SHELXL) s.res file contents are displayed for detailed inspection. 
  • SHELX-LPS: The current shelxl.lst listing is converted into the PostScript formatted file shelxl.lps and displayed using 'ghostscript'. More browsing & printing options are available via the SYSTEM-S Options menu. 
  • 1.4.28.2 – RDF-Radius 
  • Radius settings are 2.5, 5.0, 7.5, 10.0, 12.5, 15.0. The default value is 5.0
  •                                                                                        
  • 1.4.29.18 – Gaussian Toggle
  • 1.4.30.2 – Color Toggle 
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  • 1.4.31.10 - NTRY
  • Terminate parameter entry and start flipping.
  • A Log(Fobs2) versus Log(Fcalc2) plot is created showing possible outliers.
  • A one sigma bar is added to Fobs2.
    • Chapter 2 – The PLATON Tool
    • 2.1 – Introductory  Example
    •   
    • 2.2 – On How it Works
      • 2.3 - Unit Cell Transformation
    • 2.4 - Concepts and Notions 
      • 2.4.1 - TRNS - The n.ijk symmetry operation on input
      • 2.4.2 - Disorder
      • 2.4.3 – Molecules, Residues and ARU's
      • 2.4.4 - Population parameters
    • 2.5 – Instruction  Summary
      • 2.5.1 - Directives Preceding all  Calculations 
      • 2.5.2 – GEOMETRY CALCULATIONS
      • 2.5.3 - Graphics Related Instructions
      • 2.5.4 - General Instructions
    • 2.6 – Parameter  File Standards
    • 3.1 - Introduction to PLUTON and its Design
    • 3.2 – An Introductory Example
    • 3.3 - On How it Works
      • DATA and INSTRUCTION FILES
  • 3.4 - Terms and Notions.
    • 3.5 - PLUTON Keyboard Instruction Summary
    • 3.7 - VIEW INSTRUCTIONS
    • 3.8 – Input Parameter File Standards
  • Chapter 4 - ADDSYM - Find Missed or  (Pseudo)-Symmetry 
    • General Keyboard Instruction:
    • Missed Symmetry Example #1
    •  
    • Fig. 5.1-1. Views down and perpendicular to the solvent accessible channels (green) in the crystal structure of the drug Salazopyrin.
    • 5.2 - The Algorithm
    • The VOID algorithm in PLATON was also used for the description of pore types in framework structures such as Zeolites (Kuppers et al., 2006). 
    • 5.5 - Recommended SQUEEZE Procedure
  • More details can be found in Section 1.3.3.3.
  • Five types of Fourier maps are contoured
    • Introductory  Example 
  • Implementation
  • Example of a Validation Report
  • Chapter 10 - SYSTEM-S
  • 10.2 - Implementation Requirements
  • 10.3 - DEMO run(s) of S for C(10)H(12)O(6)
  • 10.4 - Worked Example in the Guided Mode
  • 10.5 - DIRECTORY STRUCTURE of SYSTEM S
  • 10.6 - PRIMARY (RAW) DATA
  • 10.7 - OTHER TRY-IT-YOURSELF EXAMPLES
  • 10.8 - How to Implement the new Space group suggested by ADDSYM
  • 10.9 - How to run S on a 'CIF/FCF' Dataset
  • 10.10 - KappaCCD/Denzo to PLATON/SYSTEM-S interface
  • 10.11 - SUMMARY OF S-INSTRUCTIONS
    • 10.11.1 - ABSGAUSS
    • 10.11.2 - ABSTOMPA
    • 10.11.3 - ASYM (VIEW)
    • 10.11.4 - AUTO
    • 10.11.5 - DIRDIF
    • 10.11.6 - EXOR
    • 10.11.7 - EXORS
    • 10.11.8 - FACE
    • 10.11.9 - FORMULA
    • 10.11.10 - HATOMS
    • 10.11.11 - INVERT
    • 10.11.12 - HELENA
    • 10.11.13 - LIST
    • 10.11.14 - LOG
    • 10.11.15 - MU
    • 10.11.16 - NQA
    • 10.11.17 - PLATON
    • 10.11.18 - PLUTON
    • 10.11.19 - RELINK
    • 10.11.20 - SHELXL
    • 10.11.21 - SHELXS86
    • 10.11.22 - SHELXS
    • 10.11.23 – SIR97 & SIR2004
    • 10.11.24 - SPGR
    • 10.11.25 - TRMX/TRNS
    • 10.11.26 - Z
    • Appendix I - Recognized Coordinate Data Input Standards 
      • A-I.1 – SPF FILE RECORD TYPES
      • A-I.2 - ANGSTROM DATA FORMAT
    • A-I.3 - The SHELX Style RES Format
    • Appendix II - Recognized Reflection File Data Formats
      • APPENDIX III - SPACE GROUP SYMMETRY
      • APPENDIX IV -  Radii Used in PLATON 

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