The platon crystallographic package
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- Bu səhifədəki naviqasiya:
- - NOSF
- CALC ADDSYM EQUAL . Sub-Menu 0 – (Section 1.4.26
- CALC ADDSYM EXACT. Sub-Menu 0 – (Section 1.4.26
- CALC ADDSYM PLOT . Sub-Menu 0 – (Section 1.4.26
- CALC NEWSYM or CALC NEWSYM 0.3 to change the allowed angular error to 0.3 from the default 0.2 Deg. EXAMPLE
- 1.3.4.7 – NONSYM - Search for and analysis of non-crystallographic symmetry
generated. - NOSF - Do not write explicit scattering factor data. (Default: do). - KEEP – Keep Monoclinic Cells with beta closer to 90 degrees (Default: Transform) - ang - Angle criterium in search for metrical symmetry of the lattice (default 1.0 degree ). - d1 - Distance criterium for coinciding atoms for non-inversion (pseudo)symmetry elements (default 0.25 Angstrom). - d2 - Distance criterium for coinciding atoms for (pseudo) inversion symmetry (default 0.45 Angstrom for organic compounds, 0.25 Angstrom for inorganic compounds). - d3 - Distance criterium for coinciding atoms for (pseudo) translation symmetry (default 0.45 Angstrom for organic compounds , 0.25 Angstrom for inorganic compounds). - perc – Allowed percentage of non-fitting atoms for a given symmetry element. The default is 20%. Sub-Menu #0 – (Section 1.4.26) – Options 1.3.4.2 - ADDSYM EQUAL This is a predefined version of the ADDSYM Tool (see Section 1.3.4.1) in which all non-hydrogen atoms are treated equal. This option can be useful when the definite atom type assignment is unclear or not done yet in the preliminary phase of a structure determination. Not all atoms are required to have a fitting symmetry companion. This feature can be invoked either by clicking on ADDSYM- EQL or with the keyboard instruction CALC ADDSYM EQUAL. Sub-Menu #0 – (Section 1.4.26) – Options 1.3.4.3 - ADDSYM EXACT This is a predefined version of the ADDSYM Tool (see Section 1.3.4.1) in which it is required that all atoms fit within the tolerances the proposed higher symmetry. This feature can be invoked either by clicking on ADDSYM-EXT or with the keyboard instruction CALC ADDSYM EXACT. Sub-Menu #0 – (Section 1.4.26) – Options 1.3.4.4 - ADDSYM PLOT This is a predefined version of the ADDSYM Tool (see Section 1.3.4.1) in which the data are averaged according to the proposed higher symmetry group and the result shown with a PLUTON style drawing. This feature can be invoked either by clicking on ADDSYM-PLT or with the keyboard instruction CALC ADDSYM PLOT. Sub-Menu #0 – (Section 1.4.26) – Options 1.3.4.5 - ADDSYM SHELXL This is a predefined version of the ADDSYM Tool (see Section 1.3.4.1) in which the data are averaged according to the proposed higher symmetry group and written as a shelxl.res. This feature can be invoked either by left-button mouse-clicking on ADDSYM-SHX or with the keyboard instruction CALC ADDSYM SHELX NOSF. Sub-Menu #0 – (Section 1.4.26) – Options. 1.3.4.6 – NEWSYM – Determine Space Group from F(calc) Model Data This is an alternative space group symmetry checking approach based on structure factors calculated from the input model. This alternate approach can be useful to detect the 'real' symmetry for a model derived from poor (possibly twinned) data using the same algorithms used to determine the space group from extinctions in observed data (also used by SYSTEM-S). NEWSYM can be invoked either with a left-button-click on NEWSYM or with the keyboard instruction: CALC NEWSYM or CALC NEWSYM 0.3 to change the allowed angular error to 0.3 from the default 0.2 Deg. EXAMPLE Following is the output of an example NEWSYM run. The input was a CIF-file. :: TITL shelxl :: CELL 19.2160 9.6890 18.6810 90.000 102.919 90.000 3390.0 :: SPGR C2/c :: Resd = 1, Z = 4, C36 H46 In2 N4 :: Moiety_Formula C36 H46 In2 N4 :: Formula_Z = 4 :: SpaceGroup_Z = 8 :: Formula_Z' = 0.500 :: mu(MoKa) = 13.9 cm-1 = 1.39 mm-1 NEWSYM - Determine Symmetry from F(calc) data(Resol = 0.60) for: shelx ================================================================================ Analysis of General Reflections for Bravais Centering Nr Ex. Condition < I/sig(I) > Number of Refl I/sigI .T/F. .True. .False. .True. .False. Max.F. H K L Ratio ============================================================================== 1 E HKL:H+K=2N 482.01 0.00 6135 0 0.00 0 0 0 99.0 Possible 2-Fold Axes - 2-Axis Crit = 0.50, Exp. Error = 0.30 Deg., LATT = C ------------------------------------------------------------------------------- Rows Products Angle Between Two Direct Axes Nr D N Direct Recip Dot Delta 1 2 3 4 5 6 7 8 9 -------------------------------------------------------------------------------- 1 9.689 0 1 0 0 2 1 0 2 0.002 0. ==== Transformation Matrix: Input (a,b,c) to Conventional Cell(a', b', c') ==== =============================================================================== (a') ( 1.00 0.00 0.00) (a) (x') ( 1.00 0.00 0.00) (x) Metrically (b') = ( 0.00 1.00 0.00) (b). (y') = ( 0.00 1.00 0.00) (y). monoclinic (c') ( 0.00 0.00 1.00) (c) (z') ( 0.00 0.00 1.00) (z) FOM: 0.002 Latt a b c Alpha Beta Gamma Volume ------------------------------------------------------------------------------- Input Cell C 19.216 9.689 18.681 90.00 102.92 90.00 3390.06 Reduc Cell P 9.689 10.760 18.681 78.48 90.00 63.24 1694.96 Conv. Cell mC 19.216 9.689 18.681 90.00 102.92 90.00 3390.06 Nr Ex. Condition < I/sig(I) > Number of Refl I/sigI .T/F. .True. .False. .True. .False. Max.F. H K L Ratio ============================================================================== 1 E HKL:H+K=2N 482.01 0.00 6135 0 0.00 0 0 0 99.0 7 E 0KL:K=2N 647.04 0.00 190 0 0.00 0 0 0 99.0 10 E H0L:H=2N 929.20 0.00 199 0 0.00 0 0 0 99.0 11 E H0L:L=2N 929.20 0.00 199 0 0.00 0 0 0 99.0 12 E H0L:H+L=2N 929.20 0.00 199 0 0.00 0 0 0 99.0 15 E HK0:H+K=2N 536.69 0.00 380 0 0.00 0 0 0 99.0 16 E H00:H=2N 1475.70 0.00 22 0 0.00 0 0 0 99.0 17 E 0K0:K=2N 701.42 0.00 10 0 0.00 0 0 0 99.0 18 E 00L:L=2N 1209.73 0.00 10 0 0.00 0 0 0 99.0 Candidate Space Groups ====================== L C N Name # AbsFreq StandSet. R(av)% N A/C-Prob ------------------------------------------------------------------------------- SPGR 2 1 1 Cc 9 844 Cc ABC 0.00 2752 39 SPGR 2 2 1 C2/c 15 5965 C2/c ABC 0.00 2752 61 1.3.4.7 – NONSYM - Search for and analysis of non-crystallographic symmetry A search for non-crystallographic symmetry in a structural model is done on two levels 1. Intra-molecular The point group symmetry of isolated molecules (residues) is determined following the SYMMOL algorithm of T. Pilati & A. Forni, J.Appl.Cryst. (1998), 31, 503-504. Examples: bucky.spf gives pointgroup Ih for C60. c476.spf gives pointgroup Td for C476. Note: - Hydrogen atoms are left out of the analysis. - The analysis is done for each discrete residue, starting with a distance tolerance of 0.1 and stepping up by 0.1 up to 0.8 until symmetry is detected. - The starting point of the tolerance can be given optionally on the keyboard instruction. Example: CALC NONSYM 0.5 Sample output of NONSYM/SYMMOL for cubane (space group R-3, site symm -3). ================================================================================ SYMMOL: Search for (additional) Molecular Symmetry Yüklə 5,01 Kb. Dostları ilə paylaş:
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