Turbo-Frodo is a general-purpose molecular modeling environment. It is designed for people who need to model de novo macromolecules, polypeptides, and nucleic acids, by building up these macromolecules from experimental X-ray crystallographic and NMR data and displaying the resulting models in various forms. These forms include Van der Waals and Connolly's molecular dot surfaces as well as spline line surfaces and secondary-structure representation. Compact views are possible, including CPK, icosahedra, and ball-and-stick styles, either individually or in various combinations.
Turbo-Frodo can color molecules, either objectively or subjectively, in order to compare them with existing structures and to evaluate their geometry. Turbo-Frodo can also fit and stack proteins, interactively mutate or chemically modify a protein, and assess the resulting conformational changes.
Turbo-Frodo reads and displays X-ray density maps. Electron density maps are calculated using the Mappage program, which is supplied along with Turbo-Frodo, giving a choice between 5 maps with 5 levels displayed on the screen. Skeletal maps are used as templates to start building up molecules with homologous protein fragments. A set of Crystallize options are available for various purposes, such as fitting molecules into electron density maps, taking the symmetry of molecules into account, and depicting molecular packing with water-accessible surfaces. These options can be used to evaluate the size of crystal channels and to decide whether diffusion or cocrystallization is the most feasible way to fit a ligand into the target protein.
Turbo-Frodo also reads and displays NMR spectra processed on Brucker equipment and displays on the screen any or all of the NMR constraints that were used to calculate a structure as well as the residual violations. A model can be interactively corrected in order to satisfy these NMR constraints while checking whether the geometry is accurate. Each residue, or even each atom, can be colored differently depending on the number of constraints in which it is involved.
With Turbo-Frodo, molecules are displayed full screen, and the functions take the form of pull-down menus, which are displayed only when they are needed. Turbo-Frodo enables the user to interact directly with a molecule via these pull-down menus and dials. Plot files can be generated on Postscript files, which can be printed out on any Postscript laser printer, such as that of a MacIntosh.
This software program is written in C language, making maximum use of the vast computing and graphics potential of the latest graphics workstations based on the Silicon Graphics Library. This is a brand new program, apart from few routines such as REFINE and RIGID, which were previously part of Frodo. "Frodo" is included in the name of the new program not for code-homology reasons but simply because Turbo-Frodo is able to deal with Frodo style electron-density maps.
Turbo-Frodo is a graphic display program built onto a data base, the Heap File, in which molecules can be stored. The Heap File is a non-finite arborescent molecular data base that is limited in size only by users' disk capacity. Turbo-Frodo users can therefore have access to all the structures stored in the Protein Data Bank (PDB), providing they have enough space on their disk .
What follows are a few notes about symbols
Symbols and stylistic matters
Stylistic matters that are used in this manual:
Quotation marks
Quotation marks: Whenever you come across quotation marks in the examples given in this manual, this means that you have to replace what is in quotation marks by the name of the file that you would like to use by simply typing the name of your file. For example, if you would like to display the structure of trypsin, the instruction turbo>load "molecule"means that you have to type turbo>load trypsin.
Bold-faced type
Bold-faced type: Bold-faced type used in this manual means that you have to type the words, letters, or characters that are in boldface. For example, if instructions in the text tell you to use the turbo> read pdb command, this means that you have to type the letters "read pdb" after the prompt sign. Bold-faced type is also used in this manual for names of files, directories, subdirectories, programs, and commands in order to distinguish them from text matter.
Uppercase letters
Uppercase letters: Words that are written in uppercase letters mainly indicate program options.
Brackets
Brackets: Brackets indicate the default answer. For example, in the Textport order FREAD PDB [WH], WH is the default answer. Generally speaking, whenever you enter a command, the default answer, if any, is indicated in brackets.
Pound sign
Pound sign: The pound sign (#) generally stands for the data base number of the molecule.
Star sign
Star sign: Two stars (**) indicate a submenu or sub-submenu. The two stars generally appear in a list of options below a menu title and thus indicate a submenu, or sub-submenu, with options of its own.