晶体结构立体模型建构软件-Diamond的使用

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矿武
5 years ago
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1 -Diamond

2 -Diamond Diamond NaCl NaCl NaCl Fm-3m(225) a=5.64å Na:4a, Cl:4b File New OK

3 Diamond1 New Structure Crystal Structure with cell and Spacegroup Cell length 5.64 Space group NaCl Fm-3m(225) Browse Fm-3m(225) Fm-3m(225) OK

automaticly Start structure picture Diamond1>Structure1>Picture1 NaCl Structure

4 Atomic parameters Completing the new structure Assistant Start structure picture; Launch the structure picture creation assistant; Create structure picture automaticly Start structure picture Diamond1>Structure1>Picture1 NaCl Structure Atomic Parameters Insert Element Na Symbol Oxidation S.O.F NaCl Na Cl 1 1 Position 4a Append Element

5 Cl Position 4b Build Fill unit cell NaCl Move Rotate along x/y axis Diamond Picture Layout Background Background Picture1 Apply now

6 Picture Atom Designs Atom Group Designs Style and colors Style Solid/Empty/Boundary ellipse Fix Color Na Cl Model and Radii Global/Individual Standard(Ball and Stick - Radii Radius[Å] for the Standard Picture Cell Edges Design Cell Edges Design Show the unit cell axis a, b, c a, b, c Objects Coordinate System Coordinate System Display Coordinate System OK NaCl Cl - Na + Cl - NaCl Build Polyhedra Add Polyhedra Add Polyhedra Central atom groups Na Na + Ligand atom groups Cl Cl - Fixed Rmin[Å] Rmax[Å]

7 Design Polyhedra Design Style and colors Others Ligand atom reducing <1 =1 >1 OK Na + Move No tracking Na + Build Polyhedra Add Polyhedra Add Polyhedra Central atom groups Ligand atom groups Cl

8 OK Esc Move No tracking File Save as Save Document as File Save as Save Structure as Diamond 3 document (*.diamdoc) Demo File Save as Save Graphics as.bmp.jpg

$c60 1.CIF 2 c60 c60 3 Add atoms 4 dummy 5 6 File Open C:\Program Files\Diamond Tutorial All Files(*.*) CIF(*.$

9 c60 1.CIF 2 c60 c60 3 Add atoms 4 dummy 5 6 File Open C:\Program Files\Diamond Tutorial All Files(*.*) CIF(*.CIF) c60 File Import Assistant File Format File Crystallographic Information File(CIF) Picture Creation If the dataset is a crystal Create a blank picture c60>s >picture1 Data brief c60 Build Fill unit cell c60 c60 60 c c60 c60 Build Connect Atoms c c60 Complete Fragments c60 c60 Picture Bond Design Bond Group Designs c-c

10 c60 Build Add atoms Add atoms c OK c Complete Fragments c c60 ( c Build Coordination Spheres Coordination Spheres Apply now c60 ) c60 c60 c60 c60 No Tracking Structure Insert Atom Insert Atom dummy c OK c60 Rmax[Å] 3 Tools Measure Distances dummy Å Rmax[Å] Border Weight 0 Add Polyhedra Angle epsilon[deg], used to extend triangles to higher polygons 10 c60 c60 dummy dummy c60 Structure Insert Atom dummy 14

dummy Statistic Connectivity Rmin[Å] Rmax[Å] Dmin[Å] Dmax[Å] Dmin[Å] 0.5 Dmax[Å] 1.

11 Complete Fragments c60 dummy dummy Rmin[Å] Rmax[Å] Build Connectivity Connectivity Select atom group pair(s) to be connected c? dummy Statistic Connectivity Rmin[Å] Rmax[Å] Dmin[Å] Dmax[Å] Dmin[Å] 0.5 Dmax[Å] 1.5 OK Build Polyhedra Add Polyhedra Add Polyhedra Generic(spheres from connectivity list) Central atom groups? dummy Ligand atom groups C 14

12 OK dummy dummy Structure Atomic Parameters Atomic Parameters dummy Element Ac dummy Complete Fragments dummy dummy c60 dummy B c60 14

$1 Filter 2 Fixed Spheres Diamond File Open C:\Program Files\Diamond Tutorial CIF(*.$

13 1 Filter 2 Fixed Spheres Diamond File Open C:\Program Files\Diamond Tutorial CIF(*.CIF) faujasite ( ), Picture, Fd-3m(227) 1 2 CIF Diamond CIF 2 Structure Space-group Space-group Fd-3m(227) + Fd-3m(227) Fd-3m(22701) Diamond Filter Build Filter Filter Atom groups SiAl Bravais translations 1:+(0,0,0) 14

OK Picture F Filter Add Atoms SiAl OK Complete Fragments Connectivity Dmax 3.2 Picture Bond Designs SiAl-SiAl Picture Viewing direction Viewing direction h k l 1, set dummy Connectivity SiAl?

14 OK Picture F Filter Add Atoms SiAl OK Complete Fragments Connectivity Dmax 3.2 Picture Bond Designs SiAl-SiAl Picture Viewing direction Viewing direction h k l 1, set dummy Connectivity SiAl? dummy Dmax 4.95 dummy SiAl 12 dummy Connectivity SiAl dummy Dmax dummy SiAl dummy c60 Complete Fragments dummy Diamond Filter dummy Build Fixed Spheres Fixed Spheres Rmax 4 Apply this function to All atoms in structure picture OK dummy dummy 14

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untitled 2006 6 Geoframe Geoframe 4.0.3 Geoframe 1.2 1 Project Manager Project Management Create a new project Create a new project ( ) OK storage setting OK (Create charisma project extension) NO OK 2 Edit project