====== Functionality ====== \\ * **###Molecular File formats:###** * ###BA - BioAdviser document - a native BioAdviser file format. Binary, proprietary format.### * ###PDB, ENT - [[http://www.rcsb.org|Brookhaven Protein Data Bank]] file format (read/write).### * ###MOL - MDL molecular file format (read/write).### * ###HIN - HyperChem data file (read only). HyperChem is trademark of HyperCube, Inc.### * ###XYZ - A simple Cartesian molecular file format (read/write).### * ###DAT - [[:chemistry_materials_life_science/products/mo-g|MOPAC]] Z-matrix files (read/write). [[:chemistry_materials_life_science/products/mo-g|MOPAC]] Cartesian format is available for writing.### * ###ARC - [[:chemistry_materials_life_science/products/mo-g|MOPAC]] ARC (archive) file (read only).### * ###WRL - VRML files (write only).### * ###PAR - BioAdviser repository files. Facilitates the modification of program repository definitions.### * **###BioAdviser view types:###** * ###Fast 3D structure (simplified molecular rendering mode targeting very large molecules).### * ###3D structure (basic, very rich 3D molecular rendering mode).### * ###AminoAcid sequences (schematic view of aminoacid chains).### * ###Properties (protein properties plots: Hydropathic index, Hydrophobicity, Karpuls & Schulz, Emini, Hopp & Woods, Kyte & Doolittle Robson & Garnier , Dipole).### * ###Ramachandran plot.### * ###PDB Edit (this view facilitates manual editing in the PDB format).### * **###Styles for 3D structure view type:###** * __###For atoms and bonds:###__ * ###Wire Frame.### * ###Ball & Stick.### * ###Cylinders.### * ###Space Filling.### * ###Hydrogens on/off.### * __###For Proteins:###__ * ###Ribbon Wires for C atoms.### * ###Ribbon Lines.### * ###Flat Ribbons.### * ###Solid Ribbons.### * ###Tubby Ribbons.### * ###Secondary Structure Motifs.### * ###Backbone only.### * ###SideChains on/off.### * __###For DNA:###__ * ###DNA backbone.### * ###DNA Rings.### * ###DNA Ladder.### * **###Color schemes for atoms and bonds:###** * ###Default color scheme (Scheme1) - characterized by black carbon atoms.### * ###Alternate color scheme (Scheme 2) - characterized by white carbon atoms.### * ###DNA Rings.### * ###DNA Ladder.### * **###Molecular Editor features:###** * ###Copy & Paste entire molecular system or selected part.### * ###Automatic Hydrogen atoms creation.### * ###Move molecules, Rotate Side Chain, Change T-Angle, Mutate.### * ###Build Protein (from Amino Acids building blocks).### * ###Change Atom type.### * ###Delete Atom.### * ###Clipping planes, clipping spheres.### * **###Selections:###** * ###Multiple selection levels: Atoms, Residues, Molecules, Labels.### * ###Select All, Invert Selection operations.### * ###Narrowing the scope of most operations to selected objects.### * **###Computations:###** * ###Preparation of [[:chemistry_materials_life_science/products/mo-g|MOPAC]] input file.### * ###Running [[:chemistry_materials_life_science/products/mo-g|MOPAC]] as a separate process.### * ###Analysis of [[:chemistry_materials_life_science/products/mo-g|MOPAC]] calculations results.###