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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.

The on-line User Manual is available or a hard copy with the same information is available in the CSB common area.

Tutorials are described in both versions of the manual.

The Turbo-Frodo homepage has additional information.

To get started in the CSB core, log in at one of the SGI graphics workstations and type:

setup turbofrodo (or source /srv/local/setup/turbofrodo.set)

You will be asked for the name of a Heap File (*.heap) or to create a new one. (The heap file is like a binary.o or session file.) A carriage return will list existing heap files or enter the name of a new one (i.e., myprotein.heap).

Then you must load a molecule. If this is the first time for a molecule then read the pdb file. First tell TurboFrodo what kind of file to read:

>read pdb

and follow the prompts. The first question asks for a name to associate with this molecule inside TurboFrodo (i.e., myprotein). Then it will ask for the actual filename (i.e., myprotein.pdb)

If the molecule already exists in your *.heap file or you got here by reading a new pdb file type:

>load moleculename (e.g., load myprotein)

To activate the dials box, type:


and answer N (i.e. no you don't want pseudo-dials)

Then to go to the graphics screen, type:


Push the cursor to the top of the screen to activate the pull-down menus.

Press MR buttons on the mouse to return to the textport.

Mouse controls are:

L M R: To pick an atom or a bones point.
L M R: To activate a pull-down menu option.
L M R: Used in the atom-addition mode.
L M R: To pop to the next residue.
L M R: To quit display to Textport.
L M R: To shift the structure displayed so that the atom selected is centered.
L M R: This combination is still not dedicated.

Note: There is no X, Y translation dial. To perform X, Y translation use the Left-Middle mouse button to pick an atom to center on. In this way you can translate the molecule.

To save coordinates see the MAKE command.

To stop, type:


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Last Modified: Friday, 26-Mar-1999 16:36:40 EST by P. Fleming