Molecular structure programs sketch

An Intelligent Sketch Pad as Input to Molecular Structure Programs... 

TRINDLE An Intelligent Sketch Pad for Molecular Structure Programs 165... 

The molecular structure entry is performed by sketching the compounds on a graphics terminal, and then storing them as connection tables. The geometries are optimized using adapt s molecular mechanics routine, MM2 [4], the semiempirical molecular orbital program (MOPAC) [5], or a newly developed extended Huckel method [6]. 

Alternately, the commercial molecular modeling software programs such as ChemOffice (http //www.camsoft.com) can be used. The ISIS draw in sketch format (struname.skc) is first converted to ChemDraw format (struname.cdx), which is then transformed into 3D structure (struname.c3d) with Chem 3D (Chapter 14) and saved as PDB format (struname.pdb). 

The opening window of Chem3D consists of the workspace (display window where 3D structures are displayed with rotation bar, slider knob, and action buttons), the menu bar (File, Edit, View, Tools, Object, Analyze, MM2, Gaussian, MOPAC, and Window menus), tool pallette (action icons for the cursor), and replacement text box (element, label, or structure name typed in this box is converted to chemical structure). Structure hie in. mol,. pdb, or. sml can be opened and saved from the File menu. Note PDB hies saved from Chem3D do not contain residue IDs.) The accompanying program, ChemDraw, draws 2D structures (.cdx) that are converted into 3D models (.c3d) by Chem3D. The molecular sketches from ISIS Draw (. skc) have to be converted to. cdx with ChemDraw for the 3D conversion. 

The tools used in molecular construction are hand-sketching in 2-D or 3-D (where use is made of graphics devices and graphics programs) and a library of graphics blocks or structure fragments, basically retrieved from one of the databases mentioned above. 

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