ChemBio3D. Director of Software Marketing CambridgeSoft (617) Skype: jessegordon. Nov. 12, 2009
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1 ChemBio3D Tips & Tricks Jesse Gordon Director of Software Marketing CambridgeSoft (617) Skype: jessegordon 1 Nov. 12, 2009
2 ChemBio3D Tips & Tricks: Presentation Outline ChemDraw Panel Demo Toolbar Model Display Toolbar Standard d Toolbar Building Toolbar Calculation Toolbar Surfaces Toolbar Menu Bars 2
3 3 ChemBio3D Tips & Tricks: Presentation Outline via Menus
4 ChemDraw Panel - ChemDraw toolbar - Name=Struct ChemBio3D Tips & Tricks: Presentation Outline Demo Toolbar Model Display Toolbar Standard Toolbar Building Toolbar Calculation Toolbar Surfaces Toolbar Menu Bars 4
5 ChemDraw panel includes the ChemDraw menu ChemBio3D Basics: ChemDraw Panel plus Name=Struct and SMILES conversion 5
6 Ring Assemblies ChemBio3D Tips & Tricks: Name=Struct and SMILES Bridged Ring Systems 3'''-([1,1'-bi(cyclopropan)]-2-yl)-3''''- ([1,1':2',1''-tercyclopropan]-2-yl)- 1,1':2',1'':2'',1''':2''',1'''':2'''',1''''':2''''',1'''''': 2'''''',1''''''':2''''''',1''''''''-novicyclopropane Bridged Fused Ring Systems Fused Ring Systems 9,10-epidiazenoanthracene version 11: unable to name version 12: 10H-furo[3',2':5,6]pyrido [3,4-a]carbazole 6
7 ChemDraw Panel Demo Toolbar ChemBio3D Tips & Tricks: Presentation Outline - Embedding in PowerPoint - Animated GIF output Model Display Toolbar Standard Toolbar Building Toolbar Calculation Toolbar Surfaces Toolbar Menu Bars 7
8 8 ChemBio3D Tips & Tricks: Demo Toolbar
9 Live Models in PPT - Collaboration and Communication «Chem3D Embed» Embed Chem3D models in PowerPoint file Rotate and zoom Chem3D models while giving g a presentation! 9 *
10 Rock or spin molecule around each axis ChemBio3D Basics: Rock and Spin Molecule Variable speed & amplitude Create animated GIF directly within Chem3D 10 *
11 ChemBio3D Tips & Tricks: Presentation Outline ChemDraw Panel Demo Toolbar Model Display Toolbar - Perspective and Depth Fading - Stereo view and 3D Glasses Standard Toolbar Building Toolbar Calculation Toolbar Surfaces Toolbar Menu Bars 11
12 Model Display panel: ChemBio3D Tips & Tricks: Model Display Display Mode: Wire Frame Sticks Ball & Stick Cylindrical Bonds Space Filling Ribbons (protein) Cartoon (protein) 12
13 ChemBio3D Tips & Tricks: Stereo view and 3D Glasses 3D glasses available for $5 a pair at: scistore.com/scistoreproductpage.aspx?itemid=3489 Cardboard red-blue or yellow-violet glasses work too! 13 *
14 ChemBio3D Visualization Tools: Perspective Tool Perspective Tool: point-of-view within the molecule: 14 *
15 ChemBio3D Tips & Tricks: Presentation Outline ChemDraw Panel Demo Toolbar Model Display Toolbar Standard Toolbar - PDB Import/Export - Model Explorer - Copy substructures Building Toolbar Calculation l Toolbar Surfaces Toolbar Menu Bars 15
16 ChemBio3D Tips & Tricks: Standard Toolbar Open PDBs (and many other formats) Save as CDX (and many other formats) Copy as ChemDraw, or as components 16
17 ChemBio3D Basics: Online links Import PDB s from online databases: (retrieved from Brookhaven Natl. Lab) For example PDB ID = 3cee (Lipid-Binding Protein) Import structures by ACX number (ChemDraw includes Online function: Find ACX numbers from Structure e.g. X for benzene Import from ChemACX (by name or structure) 17 *
18 Model Explorer Tree Control - Efficiently explore the structure of large molecules List amino acids in PDB structures Select by chain (for surface visualization or database) Select by individual residues or multiple residues (for hydrophobicity analysis, e.g.) Select within alpha- and beta- secondary structures Select solvent (for hiding, or showing hydrogen-bonding, e.g.) 18 *
19 ChemBio3D Tips & Tricks: Copy substructures Select amino acids, or any components, even if non-contiguous 19 *
20 ChemBio3D Tips & Tricks: Presentation Outline ChemDraw Panel Demo Toolbar Model Display Toolbar Standard Toolbar Building Toolbar - Dynamic Hydrogen Bonding - Rotation Dial - Starting point for conformations Calculation l Toolbar Surfaces Toolbar Menu Bars 20
21 ChemBio3D Tips & Tricks: Building Toolbar You can draw moities and move atoms within 3D panel: 21
22 22 ChemBio3D Analysis Tools: Hydrogen Bonding Hydrogen bonding is automatically calculated based on distance between polar hydrogen and nearby oxygen or nitrogen atoms. Parameters: - Hide all H-bonds - Show all H-bonds - Show only intermolecular - Hide all H-atoms - Show all H-atoms - Show only polar hydrogen - Show lone pairs - Show atom dots
23 ChemBio3D Basics: Rotation Dial Rotate around x, y, or z axis Local rotation (around two atoms) Dihedral rotation (around one bond) Freehand rotation 23
24 ChemBio3D Tips & Tricks: Starting point for conformations Two conformations around a non-rotatable bond; energy minimization result depends on starting point. 24 *
25 ChemBio3D Tips & Tricks: Presentation Outline ChemDraw Panel Demo Toolbar Model Display Toolbar Standard Toolbar Building Toolbar Calculation Toolbar - Dihedral Driver - Lipid shape prediction Surfaces Toolbar Menu Bars 25
26 MM2 minimization and MM2 dynamics: ChemBio3D Tips & Tricks: Calculation Toolbar (other calculations areonthe calculations menu) 26
27 ChemBio3D Tips & Tricks: Dihedral Driver Dihedral driver demonstrates rotational barrier, and the two low-energy conformations 27 *
28 ChemBio3D Analysis Tools Structure Prediction Energy minimization structure predictions: Some ab initio; some semi-empirical. empirical Some included; some added in. 28 *
29 ChemBio3D Analysis Tools Structure Prediction Preliminary structure is geometric only: 29 * Simple, but live (instantly updated): in ChemDraw panel, or in Chem3D Hotlink
30 MMFF94 Force Field Minimization - Support for Protein Calculations Specifically designed to perform energy calculations and minimizations on proteins and other biological structures More Atom types and better parameters MMFF94 was parameterized as a combined organic/protein force field, and so is equally applicable for proteins, small molecules, l or systems containing i both. Additionally, the MMFF94 force field provides a richer set of atom types than MM2, so MMFF94 calculations may succeed in cases where MM2 calculations fail due to missing atom types 30 *
31 ChemBio3D Tips & Tricks: Lipid shape prediction What is the bond angle in oleic acid? 31 *
32 ChemBio3D Tips & Tricks: Presentation Outline ChemDraw Panel Demo Toolbar Model Display Toolbar Standard d Toolbar Building Toolbar Calculation Toolbar Surfaces Toolbar - Transparent and partial surfaces - Hydrophobicity surface Menu Bars 32
33 33 ChemBio3D Tips & Tricks: Surfaces Toolbar
34 34 ChemBio3D Visualizations: Surface Visualization
35 35 ChemBio3D Visualizations: Surface Transparency
36 ChemBio3D Tips & Tricks: Presentation Outline ChemDraw Panel Demo Toolbar Model Display Toolbar Standard Toolbar Building Toolbar Calculation Toolbar Surfaces Toolbar Menu Bars - Spectrum Viewer - Structure Browser - Fast Overlay 36
37 37 * ChemBio3D Extensions - Infrared spectra
38 Structure Browser Fast Overlay The Structure Browser allows users to easily flip through a collection of small molecules and compare their structures t and properties Fast overlay and manual overlay 38
39 Medicinal Chemistry Structure Browser Guided Overlay The Structure Browser allows users to easily flip through a collection of small molecules and compare their structures and properties 39
40 Overlay of biomolecules Draw a pair of tetrapeptides from BioDraw Energy-minimize in ChemBio3D Overlay the pair to see conformational differences. H Glu Cys Met Gly OH H Gln Cys Met Gly OH 40 *
41 ChemBio3D Tips & Tricks Jesse Gordon Director of Software Marketing CambridgeSoft (617) Skype: jessegordon 41 Nov. 12, 2009
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