ydkr_manu_v12.PDF
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1 Yadokari-XG Ver /02/22 4 Yadokari-XG c: ydkr elements.dat sg.dat sym.dat sym2.dat ydkr.exe ydkr.ini ysg.exe ortep3.exeortep-3 ntserver.exeortep-3 grfont.datortep-3 Yadokari-XG SHELX PATH c: windows command ciftab.def (c: ydkr ) ciftab.exe ciftab.rta (c: ydkr ) ciftab.rtm (c: ydkr ) shelxa.exe shelxh.exe shekxl.exe shelxpro.exe shelxs.exe shelxwat.exe sprint.exe SIR97DIRDIFPOV-Ray C: ydkr.exe Yadokari-XG 1
2 2 4 Display Control Panel ORTEP Part 0 AFIX AFIX SHELX Å Å SHELX
3 3 ON/OFF 3D (OpenGL) OpeGL Setup 9 4 gaussian output Shift Shift Ctrl Alt Fit Model to Window
4 4 ORTEP ORTEP Symmetric Expansion (AUTO) ExpansionExpansion AUTO LSQ LSQ LSQ ORTEPORTEP SHELX LSQcycle POV-Ray controlpov-ray control
5 SHELXL SHELXL LSQ LSQ CIF CIF LSQ ***.pdb PDB protein data bank Chem 3D 5
6 6 PDB PDB cif 2 LSQ LSQ 2 0 = 3 Fo 2 < 3σ(Fo 2 ) ACTA weight SHELX weight
7 7 4 ORTEP Boundary only Open model Football Shaded octants ORTEP Probability 50% 30% Bond Radius 0.04Å ORTEP c: ydkr elements.dat bitmap
8 4 Ball and StickSpace FillingThermal Ellipsods -( ) ***.yps 8
9 4 BbtBr yadokari-xg c: ydkr.exe Me 3 Si H Br H SiMe 3 Me 3 Si SiMe 3 Me 3 Si SiMe 3 SiMe 3 BbtBr NEW test f2.dat BbtBr.cif(crystalclear.cif ) ***.cif crystalclear.cif Crystal Clear 9
10 OK Yadokari-XG ***.cif input.head texray.inf CIF file.cif HKL f2.dat f2plus.dat f2plus.dat input.head texray.inf.cif 10
11 Crystal System Space Group Set OK Z OK.cif Z <SHELXS-97 > SHELXS-97 11
12 MS-DOS RE OK 12
13 13 Delete
14 14 <SIR-97 > SIR-97 OK EXIT Yadokai-XG Delete SHELXS-97
15 <DIRDIF-99 > DIRDIF99.2 Interface AutoPATTY FilesEXITYadokari-XG SHELXS97 SIR97 15
16 LSQ >50º SHELXL 16
17 LSQ Apply 17
18 0 10 LSQ Max. shift = A for LSQ 0 LSQ Esc Esc SHELX 18
19 19 OK Ctrl+A refine LSQ R disorder R=8% disorder
20 disorder LSQ 1 Bbt part 0 part 1, part 2.. Si4 Q1C21C20 part 1 Q2Q9C19 part 2 Q1Q2Q9 20
21 part 1 part 1 part 1 Part1 Part2 Part 2 Part 2 Si5 21
22 C22 C22C23Q4 part 1C22Q5Q6 part 2 C24 part 1 part 2 C22 part Si3 Si5 part 1part 2 part1part2 part1part2 0.5 part LSQ LSQ Apply R1 6% 1 22
23 FVAR 0.5 R part 1 part 2 1 part1 part2 1 FVAR 23
24 Si4 FVAR FVAR FVAR 1 FVAR 2 FVAR 3, 4, 5,. FVAR 3 0 FVAR FVAR OK Si4 part 1 C20, C21, C31 FVAR 2 FVAR 2 SHELX
25 part 2 C19, C32, C33 1 FVAR 2 Si3Si5 FVAR 3FVAR LSQ LSQ 0.5:0.50.4:0.6 25
26 26 HFIX, AFIX refine X AFIX AFIX33 AFIX137
27 27 AFIX33 AFIX33 AFIX AFIX AFIX HFIX SHELXL HFIX AFIX LSQ ( rest )
28 LSQ LSQ 28
29 29 OMIT
30 resolution resolution resolution1 resolution 1 D(F^2)/esd 5 OMIT R R resolution 1 Fc^2 0.3 Fo^ h, k, l= (1, 9, 12), ( 1, 3, 6) Ctrl OK LSQ 30
31 R1 4% LSQ SHELXL SHELXL SHELXL CIF LSQ CIF SHELX BOND$H 31
32 PDF pdb fileprotein data bank file LSQ ***.cif***.pdb*** CIF CCDC CIF LSQ.rtf Word crystal systemspace group 32
33 33
34 part 2 ORTEP ORTEP ORTEP Probability bond ORTEP Boundary Only bmp ORTEP OHP ORTEP 34
35 35
36 Part 2 POV-Ray Space Filling bmp Shift 36
37 4 elements.dat elements.datc: ydkr elements.dat ORTEP BIND FREE elements.dat Bi bismuth purple VdW R G B ORTEP ydkr.inic: ydkr ydkr.ini ydkr.ini POV-Ray R G B 1 100% VdW ydkr.inic: ydkr ydkr.ini # # R G B # _color_table_num 20 _define_color 'black' _define_color 'blue' _define_color 'red' _define_color 'purple'
38 _define_color 'green' _define_color 'cyan' _define_color 'yellow' _define_color 'white' _define_color 'voilet' _define_color 'brown' _define_color 'gray' _define_color 'orange' orange % _color_table_num 4 LSQ SHELXL-97 ****.ins SHELXL-97 yadokari-xg ***.ins LSQ.ins ***.ins SHELXL-97 SHELX 38
39 ***.ins σ ***.lst ***.res ***.ins P 1 (no.2) P2 1 /c -X, -Y, -Z C2/c LATT 39
40 4 SHELXL AFIX mn: C H C C C H C H C C H C C H H N H C C H H H C H H O H H C H H O C C C C AFIX33 AFIX33 d: sof: U: CH 3 OH AFIX mn AFIX SHELX 40
41 AFIX Si H1.48 Å H AFIX Yadokari-XG 41
42 4 SHELXL constraint restraint constraint restraint AFIX constraint AFIX constraint restraint Σw(Fo 2 Fc 2 ) 2 Σw(Fo 2 Fc 2 ) 2 +Σw(y t y) 2 y t y w=1/σ 2 SHELXL σ restraint σ restraint restraint s d σrestraint d 0 15 d d restraint s s 1 2 σ1 1 3 σ2 restraint s σrestraint s σrestraint s s σ1 restraint 1 3 σ2 restraint σ1σ2 0 restraint s s d σ1 Uij restraint σ2 42
43 s s σ1 restraint Uij σ2 restraint restraint 4 n 2 n 1 l k h n 0 n 3 s OMIT Fo 2 [ Fo 2 < 3σ(Fo 2 )] observed s Fo 2 0 Fo 2 10 S Fo 2 <sσ(fo 2 ) ACTA cif t 2θ 2θ<50º OMIT (h k l) merge unobserved OMIT x=dx+s xy=dy+s y, z=dz+s z MOVE MOVE
44 BOND BOND$H ACTA.cif n esd esd n n Yadokari-XG SHELX MPLA Yadokari-XG MPLA 4 X cif file crystallographic information file SHELXL ***.cif CIF checkcif@iucr.org cif Acta Cryst. 44
45 45
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51 218-224 2009 Yadokari-XG 2009 G-COE Chizuko KABUTO, Shigehisa AKINE, Takashi NEMOTO and Eunsang KWON: Release of Software Yadokari-XG 2009 for Crystal Structure Analyses Yadokari-XG 2009, Yadokari-SG,
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