Model systems can be generated and manipulated fully within Scigress Explorer, or imported from a variety of commonly used file formats such as PDB (Brookhaven Protein Data Bank), MOL files, SD files, and the output of popular chemical drawing programs. Batch 2D to 3D conversions are also provided. Once the model is in the Scigress Explorer workspace, the scientist can edit it, correct or alter its geometry, invert chiral centers, and superimpose molecules. Especially valuable is the Beautify command with its many options including Comprehensive, which corrects valence, hybridization, geometry, and ring structure in a single step.
Geometric features of models can be rendered with a range of display methods such as ball and stick, tubular, and ribbons. Further analytical data and features such as measurements (e.g., bond lengths and angles, distances), surfaces, and orbitals can be added. Optional stereoscopic 3D visualization speeds the comprehension of spatial relationships.
For protein studies, model building is facilitated by sequence editing, insertion, and mutation with automatic 3D display. Proteins can be colored according to various criteria, and protein sequences can be aligned. Ligand pocket surfaces, manual docking of ligands, and an optional automated docking procedure help elucidate binding features.