| Converter |
Converter recognizes both wedged bonds and atom stereo designators in the 2D file and converts the molecules to the appropriate configuration. You also can generate both R and S conformations for centers whose chirality is unspecified in the 2D file. Multiple molecules can be generated if more than one unspecified chiral center is present. The three-dimensional conversion process can also be biased towards producing either extended or random chain conformations and towards producing either all-chair or random conformations of 6-membered rings. The output of hydrogens can be controlled with options for writing Original, Hetero, or All hydrogens to the Output_3d_File. In addition, Converter is able to correctly convert structures that consist of several pieces.
Converter can be run interactively, allowing you to view the progress of the database conversion, or in the UNIX background, for batch generation of the structures.
The Converter license is required to run Converter. When invoked via the Insight II software, Converter automatically checks out the license or informs you if it is unavailable.
Chapter 2, Theory, in Part 2 presents the theory upon which Converter is based. It is written mainly for the typical scientist-user of Converter. Chapter 3, Command Summary, briefly summarizes the main functions of each command. Chapter 4, Methodology, explains how to use Converter in both the Insight II and background modes. Appendices A, References and B, Glossary contain the scientific references cited in this User Guide and a glossary of terms and symbols. The file formats and a utility are documented in Appendices C, File Formats, and D, Utilities, respectively. For information about MDL file formats, please refer to your MDL documentation.
Using This Guide
In addition to this printed Converter documentation, on-line help is available and activated by clicking the ? icon in the Insight II window.
Additional Information
In referring to commands that are used when running Converter through the Insight II menus, this guide uses the format Pulldown/Command, since you use the mouse to select the pulldown first, before the command name appears. Note, however, that if you type commands in the Command area near the bottom of the Insight II window, the names must be entered in the format Command Pulldown or Command (whichever appears at the top of the equivalent parameter block).
Note on Command Names