ChemBioFinder 14.0 User Guide ChemBioFinder 14.0 Table of Contents Chapter 1: About ChemBioFinder 1 About BioViz 1 About this guide 1 Serial Number and Technical Support 2 Chapter 2: Getting Started 4 The ChemBioFinder User Interface 4 More UI features 10 Opening ChemBioFinder 11 Using ChemBioFinder with databases 11 Chapter 3: Tutorials 14 Sample databases 14 Tutorial 1: Creating forms 14 Tutorial 2: Opening a database 16 Tutorial 3: Creating a database 17 Tutorial 4: Searching a database 19 Tutorial 5: Reaction searches 22 Tutorial 6: Creating a BioViz plot 25 Tutorial 7: Working with subforms 29 Chapter 4: Forms 31 Creating forms automatically 31 Saving a form 32 Creating forms manually 33 Setting box properties 39 Editing forms 46 Chapter 5: Databases 58 Selecting a database 58 Opening databases 61 Table of Contents i ChemBioFinder 14.0 Browsing databases 63 Creating a database 69 Creating a portal database 75 Chapter 6: Working with Data 76 Entering data 76 Editing data 78 Sorting data 83 Resetting the database 84 Changing the database scheme 84 Chapter 7: Importing and Exporting Data 86 Supported file formats 86 Importing data 86 Exporting data 92 Chapter 8: Queries 96 Text searches 96 Numeric searches 97 Molecular formula searches 97 Date searches 99 Find list 99 Structure searches 100 Reaction searches 105 Combined searches 109 SQL searches 110 Query procedures 110 Refining a search 117 Special structure searches 120 Managing queries 124 Search examples 130 Chapter 9: Compound Profiles 135 Table of Contents ii ChemBioFinder 14.0 Creating a compound profile 136 Editing a compound profile 138 Customizing 142 Chapter 10: Chemical Properties 143 ChemBioFinder Chemical Properties 143 About Molecular Networks 144 ChemBio3D Chemical Properties 153 ChemBioDraw Properties 153 Chapter 11: Relational Data and Subforms 155 Access relational data 155 Creating a subform 155 Working with subforms 157 Searching a subform 157 Chapter 12: BioViz 160 Creating a plot 160 Viewing Plots 163 Plotting queries 164 Changing the display 166 Statistical analysis 167 Customizable styles 172 Chapter 13: Clustering in BioViz 174 Features 174 Working with Clustering 174 Modifying Clustering 176 CS Clustering Dialog features 178 Chapter 14: ChemBioFinder/Oracle 180 Setup 180 Opening an Oracle database 181 Searching 182 Table of Contents iii ChemBioFinder 14.0 Sorting 182 Handling lists 183 Setting Oracle preferences 184 Updating and adding data 184 Loading 185 Indexing 186 CAL 188 Chapter 15: BioSAR 189 Starting the BioSAR browser 189 Performing searches in BioSAR 189 Exporting the data form to ChemBioFinder 189 ChemBioFinder file types 189 Subforms and autolinks 190 Multiple sort 191 Query hit lists 192 Domains 195 Creating an mdb database 196 Chapter 16: Customizing ChemBioFinder 199 Setting preferences 199 Favorites tree 205 Toolbars 206 Periodic table 208 Embedding ActiveX controls 209 Scripting 210 Methods of communication 218 Chapter 17: Structural Query Features 222 General properties 222 Changing the scope of a search 230 Atom properties 230 Table of Contents iv ChemBioFinder 14.0 Bond properties 235 Chapter 18: Formula Input Rules 238 Rules 238 Examples 238 Chapter 19: Similarity Rules 240 Complete structure similarity 241 Substructure similarity 241 Chapter 20: CAL Commands 242 CAL help 242 Menu commands 242 Box creation commands 245 Box manipulation commands 254 Program execution commands 258 General commands 262 File commands 277 Variable commands 280 Environment variables 287 Script-only commands 288 Chapter 21: ChemScript 295 Why use ChemScript? 295 How ChemScript works 296 Getting Started 296 Editing Scripts 297 Introducing the ChemScript API 298 Tutorials 299 Useful References 302 Chapter 22: CS Oracle Cartridge 303 Fast-move caching scheme 303 Configuring via CF_SETTINGS table 304 Table of Contents v ChemBioFinder 14.0 Searching 305 Table of Contents vi ChemBioFinder 14.0 About ChemBioFinder ChemBioFinder is a database management system for anyone who works with chemical information. It provides a place to store chemical structures, physical properties, notes, tables of data, and plots. With ChemBioFinder, you can quickly find and organize your data. About BioViz BioViz is a visualization add-in for ChemBioFinder that lets you plot numeric data from ChemBioFinder databases. You can identify trends and correlations in your data without exporting to another application. You can have as many plots as you like, each showing a different visualization of data from the current form. ChemBioFinder & BioViz is integrated with these applications: ChemBioDraw. Lets you draw two-dimensional structures and reactions. ChemBio3D. Lets you view three-dimensional structures. ChemBioDraw/Excel. Lets you export data to MS Excel. About this guide The topics in this user guide are organized by task. They are intended to help you familiarize yourself with the ChemBioFinder applications and start using them as quickly and efficiently as possible. New users should read the Getting started chapter for an overview of the product and how it works. The Tutorials chapter demonstrates most of the features of the application. Perform the tutorials in the order they are presented. Experienced users can skip to sub- sequent chapters, which provide more detailed information. This guide assumes that you are familiar with the basics of your Windows operating system. If you are not, refer to your system manual. Some of the material describes tasks that must be performed in conjunction with other integrated ChemBioOffice products. The material on the addins describes tasks that must be performed in conjunction with Microsoft Excel or Word. If you are not familiar with these applications, consult the relevant user’s manual. Conventions The following notations are used throughout this guide: Caution: Cautions warn you of situations that might cause a possible loss of data. Note: Notes highlight important information. Tip: Tips are helpful hints that supplemental the main text. Shortcut key sequences are indicated with a + sign, for example: “Use the command: CTRL+H to toggle hidden Hydrogens and lone pairs.” A bold font is used to refer to the User Interface, for example “Go to File>Save”. Chapter 1: About ChemBioFinder 1 of 305 ChemBioFinder 14.0 Serial Number and Technical Support The serial number is a unique key that helps you install and activate the ChemBioOffice application on your computer. This is the same number you entered when you launched your ChemBioOffice application for the first time. If you have lost your installation instructions, you can find the serial number from the application. Go to Help>About <ChemBioFinder>.The serial number appears in the dialog box. For more information on obtaining serial numbers and registration codes, see the online Services Web site. Technical support is available to registered users through the Internet and our Technical Support department.When contacting Technical Support, always provide the serial number of your ChemBioOffice application. Our Technical Support Web pages contain answers to frequently asked questions (FAQs) and other information. To access our Technical Support in ChemBioFinder, go to Online>Browse CambridgeSoft Technical Support. If you are unable to find a solution on the Web site, follow these steps before you contact Technical Support: 1. Check the system requirements for the software. 2. Read "Troubleshooting" on page 2 and follow the possible resolution tactics outlined there. 3. If all your attempts to resolve a problem fail, contact Technical support. Try to reproduce the problem before contacting us. If you can reproduce the problem, please record the exact steps. Record the exact wording of any error messages that appear. Record what you have tried to correct the problem. Additional sources of ChemOffice information are: ChemBioFinder online Help The PerkinElmer Informatics Web site PerkinElmer Informatics Services Troubleshooting This section describes steps you can take that affect the overall performance of CS ChemBioOffice Applications, as well as steps to follow if your computer crashes when using a CS software product. Performance Below are some ways you can optimize the performance of ChemBioOffice Applications: In the Performance tab in the System control panel, allocate more processor time to the application. Install more physical RAM. The more you have, the less ChemBioOffice Applications will have to access your hard disk to use Virtual Memory. Increase the Virtual Memory (VM). Virtual memory extends RAM by allowing space on your hard disk to be used as RAM. However, the time for swapping between the application and the hard disk is slower than swapping with physical RAM. Chapter 1: About ChemBioFinder 2 of 305 ChemBioFinder 14.0 Applications and Drivers As with most complex software applications, there may be unusual circumstances in which ChemBioFinder may become unresponsive. Below are some recommended steps for you to follow to try to resolve software and driver issues. 1. Restart Windows and try to reproduce the problem. If the problem recurs, continue with the following steps. 2. The most common conflicts concern video drivers, printer drivers, screen savers, and virus protection. If you do need to contact us, be sure to determine what type and version of drivers you are using. Video Driver related problems: If you have problems displaying any ChemBioOffice Application, try switching to the VGA video driver in the display Control Panel or System Setup, and then retest the problems. If using a different driver helps, your original driver may need to be updated–contact the maker of the driver and obtain the most up-to- date driver. If you still have trouble, contact us with the relevant details about the original driver and the resulting problem. Printer Driver related problems: Try using a different printer driver. If using a different driver helps, your original driver may need to be updated–contact the maker of the driver and obtain the most up-to-date driver. If you still have trouble contact us with the relevant details about the original driver and the resulting problem. 3.