• Reset: Reset all windows and start a new structure.
• Open...: (⌘O) 'FoldIt (light)' can read directly any protein coordinate text file from the Brookhaven Protein Data Bank (PDB) (Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F.Jr, Brice, M.D., Rodgers, J.R., Kennard, O., Shimanoughi, T., & Tasumi, M. (1977) J.Mol.Biol. 112, 535-542) including hetero-atoms and water molecules. This implies that files have a TEXT format and are ended by one of the suffixes '.PDB', '.pdb' or '.ent' (e.g. 1CRN.PDB, pdb1crn.ent). Normally these files begin with the word 'HEADER'. If they don't they will still be read (at a somewhat slower speed). In all cases, the program recognizes only the PDB nomenclature. FoldIt can save any structures in their own binary formats (suffix '.FIT') which are of course much faster to read and contain the complete hydrogen-bonding pattern of the protein.
Holding the OptionKey down while opening a file displays a dialog to read only part of that file or only selected residues.
To read a second structure into memory while keeping the one which has just been read, hold down the Control key while selecting the Open... menu item.
• Close EDmap...: Close the electron density map in memory (only one map can be read in memory at a time). Feature not available on all versions.
• Delete...: Delete a file.
• Save: Save the changes applied to an already existing '.FIT' file.
• Save As...:
* Picture: Save front window picture (the Image window, or any of the utility windows providing they contain PICT information) on disk;
* Report: Save text content of Report window on disk.
* Histograms: Save content of ALL histogram windows in a unique PICT file on disk.
* .FIT: Save the current structure into a binary file. If 2 structures are in memory, a dual file (containing both structures) will be created.
* .PDB: Save the current structure into a text file (usual PDB format) which name terminates by one of the suffixes '.PDB', '.pdb' or '.ent'. Only the coordinates of the displayed atoms are stored. It is thus possible to create 'main-chain-only' files or 'backbone-only' files.
* .SEQ: Save only the current sequence into a text file. If 2 structures are in memory, a dual file (containing both structures) will be created.
* .EDFIT: Save the current electron density map (text) into a binary file. Feature not available on all versions.
* .RamW: Save the current RamW in a file which will be recognized by 'FoldIt (light)'.
* .SSBdW: Save the current SSBdW in a file which will be recognized by 'FoldIt (light)'.
* .HBdW: Save the current HBdW in a file which will be recognized by 'FoldIt (light)'.
* .StatW: Save the current StatW in a file which will be recognized by 'FoldIt (light)'.
* .AroundW: Save the current AroundW in a file which will be recognized by 'FoldIt (light)'.
* .MotivW: Save the current MotivW in a file which will be recognized by 'FoldIt (light)'.
* .Anim: Save the current animation in a file which will be recognized by 'FoldIt (light)'.
• Pause: Pause lengthly batch procedures to momentarily direct CPU time towards other running applications.
• Abort: (⌘A) Abort user requested operations (To abort a structure motion, just press any key or click the mouse).
