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Administrator 7. Leave the last line in the data file blank to indicate file termination. 8. Save the file in a text only format. MOPAC Graph Files A MOPAC Graph (GPT) file stores the results of MOPAC calculations that include the GRAPH keyword. It contains the final geometry, electronic structure, and other properties of the molecule. Chem3D supports the MOPAC Graph file format for import only. Protein Data Bank Files Brookhaven Protein Data Bank files (PDB; ENT) are used to store protein data and are typically large in size. Chem3D can import both file types, and exports PDB. The PDB file format is taken from the Protein Data Bank Atomic Coordinate and Bibliographic Entry Format Description. ROSDAL Files (RDL) The ROSDAL Structure Language 1 (RDL) file format is defined in Appendix C: ROSDAL Syntax of the MOLKICK User’s Manual, and in this manual in Appendix F, “File Formats.” on page 640. The ROSDAL format is primarily used for query searching in the Beilstein Online Database. Chem3D supports the ROSDAL file format for export only. Standard Molecular Data (SMD) Use the Standard Molecular Data (.SMD) file format for interfacing with the STN Express application for online chemical database searching. Both import and export are supported. 1. ROSDAL is a product of Softron, Inc. SYBYL Files Use the SYBYL © (SML, SM2, ML2) file formats to interface with Tripos’s SYBYL applications. The SML and SM2 formats can be used for both import and export; the ML2 format is supported for import only. Tinker MM2 and MM3 Files Use the XYZ file format to interface with TINKER © software tools. Specify MM2 for most models, MM3 for proteins. Both import and export are supported. Job Description File Formats You can use Job description files to save customized default settings for calculations. You can save customized calculations as a Job Description file (.JDF) or Job Description Stationery (.JDT). Saving either format in a Chem3D job folder adds it to the appropriate Chem3D menu. JDF Files The JDF file format is a file format for saving job descriptions. When you open a JDF file, you can edit CSBR and save the settings. JDT Files The JDT file format is a template format for saving settings that can be applied to future calculations. You can edit the settings of a template file, however you cannot save your changes. 122•Printing and Exporting Models <strong>CambridgeSoft</strong> Job Description File Formats
Exporting With the Clipboard The size of the file that you copy to the clipboard from Chem3D is determined by the size of the Chem3D model window. If you want the size of a copied molecule to be smaller or larger, resize the model window accordingly before you copy it. If the model windows for several models are the same size, and Fit Model to Window is on, then the models should copy as the same size. Transferring to ChemDraw You can transfer information to ChemDraw as a 3D model or as a 2D model. To transfer a model as a 3D picture: 1. Select the model. 2. From the Edit menu, point to Copy As, then choose Picture. 3. In ChemDraw, select Paste from the Edit menu. NOTE: The model is imported as an EMF graphic and contains no structural information. To transfer a model as a 2D structure: 1. Select the model. 2. From the Edit menu, point to Copy As, then choose ChemDraw Structure. 3. Open ChemDraw. 4. From the Edit menu, choose Paste. The model is pasted into ChemDraw. Transferring to Other Applications To copy and paste a space-filling model into a word processing, desktop publishing, presentation or drawing application, such as Microsoft Word or PowerPoint: 1. Select the model. 2. From the Edit menu, point to Copy As, then choose Picture. 3. Paste the model into the target application document. TIP: If you are pasting into MS Word or PowerPoint, select Paste Special and choose the type of graphic you wish to import: bitmap, WMF, or EMF. The EMF option will copy with a transparent background. Alternatively, you could use Save As Bitmap or EMF to create a file to insert into or link to the target application document. <strong>ChemOffice</strong> 2005/Chem3D Printing and Exporting Models • 123 Exporting With the Clipboard
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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Administrator Connection Table . .
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Administrator Specifying Properties
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Administrator Undoing Changes . . .
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Administrator Chapter 28: Introduci
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Administrator Atom Properties . . .
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Administrator Deleting a Field Type
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Administrator Example 2. . . . . .
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator 250•ChemFinder Tuto
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The Open dialog box appears. To cho
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A data source tree appears, contain
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Parameter Table Use Parameter Table
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Administrator xxxviii• CambridgeS
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CAMBRIDGESOFT ChemOffice Desktop to
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CS ChemOffice Software Suites ChemO
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DESKTOP CS ChemFinder Searching and
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ENTERPRISE ChemOffice WebServer Ent
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KNOWLEDGE E-Notebook Enterprise Des
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KNOWLEDGE Document Manager Desktop
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KNOWLEDGE 21CFR11 Compliance Electr
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RESEARCH & Registration System Chem
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RESEARCH & Inventory Manager Chemic
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RESEARCH & CombiChem Enterprise Des
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CHEMICAL ChemACX Database Available
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CHEMICAL The Merck Index Chemistry
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CHEMICAL Chemical Databases Referen
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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