• FoldIt Balloons: (⌘?) Toggles the application Balloon Help.
• FoldIt Help: This is an in-line help (thanks to R. Fronabarger) which contains the same information as the 'FoldIt User Manual'.
File menu
• 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).
• Quit (⌘Q).
Edit menu
Executes usual editing procedures (applies only to Report window).
• Preferences...: User's preferences are set through this dialog.
'Open Structure in Full Screen': this automatically fits each structure to the image window; 'Includes H-atoms': Include (or not) H-atoms in saved structures; 'Show Clash Between Atoms During Torsion': on top of visualizing the clashes between atoms it predict them in the Report window; 'Write File Header': refers to the header preceding PDB files. Turn it off when you batch process files; 'Report Operations': every step is reported in the Report window. Turn it off when you batch-process files.
You can adapt to your environment the text and graphic outputs of 'FoldIt (light)' by changing the PICT and TEXT signatures with the two 'Set...' buttons. By default these signatures are set to 'TeachText'.
Build menu
• Experimental Settings...: The presence of protons depends on pH. Other parameters are also included.
• Add Block: Add any residue/base at the end of a structure. This way, a structure can be started from scratch by building the polypeptide chain (or a nucleic acid chain) in a completely extended form (j=y=180°). 'Add Block' adds also a given sequence to a PDB structure already in memory.
Adding bases has not been yet implemented.
• Mute Block...: Perform site directed mutagenesis on a selected residue (it is not yet implemented for bases). A single residue must have been selected (Control Click). Conformation of main chain atoms and of side chain Cb is preserved.
• Enter/Add Sequence...: Type (or paste) in the one-letter code sequence to be built from scratch or added to a structure already in memory.
• Add Last Block: (⌘Y) Repeat the last entered residue/base.
• Undo Last Block: (⌘U) Undo sequentially the structure in memory.
• Turn Bond: (item enabled only if a torsion atom has been selected by double-clicking on an atom with the Option key down)
If the 'Show Clash Between Atoms During Torsion' has been set in the File/Preferences dialog, clashed atoms are marked as torsion proceeds.
* ClockWise, CounterCW: (‚åòS, ‚åò/) Torsion direction around the torsion atom.
* Go Crazy: randomly(?) turn all bonds of a structure.
• Step Folding: Display residue after residue the folding of a structure (use ⌘Y to do this). If the OptionKey is down when choosing this menu item, the folding is not automatic but occurs stepwise (use ⌘Y to enter one residue at a time).
Structural information concerning each residue is given:
region (region of Ramachandran plot): pack (helix region), packG (symetrical of helix region), extd (sheet region), extdG (symetrical of sheet region), out (none of the preceeding);
state : alpha, 310, strand, turn, coil;
phi : phi angle in degree.
psi : psi angle in degree.
chi1 : chi1 angle in degree.
OBded: indicates to what atom(s) main chain oxygen is H-bonded (Bded= bonded).
NBded: indicates to what atom(s) main chain nitrogen is H-bonded.
SCBded: indicates to what atom(s) side chain atoms are H-bonded.
• Fold Into Helix.
Utilities menu
• Batch File Settings...: Dialog to limit the quality (resolution, refinement) and type of files which will be considered during a batch process.
Data bases can also be selected (Feature not available on all versions.): 'Boberg Files' are the files listed by Boberg, J., Salakoski, T., & Vihinen, M. (1992) Proteins 14, 265-276, 'Stickle Files' are the ones listed by Stickle, D.F., Presta, L.G., Dill, K.A., & Rose, G.D. (1992) J.Mol.Biol. 226, 1143-1159 and 'Swindells Files' are the ones listed by Swindells, M.B., MacArthur, M.W., &Thornton, J. (1995) Nature Struct.Biol. 2, 596-603. Thus if the option 'Boberg Files' has been selected, only the files belonging to this group and located in the 'Batch Fldr' will be considered in statistics.
• StdW Settings... (Standard Window Settings):
Profiles:Energy Maximum & Profiles:Auto Scaling: Used to scale 'Top Profile' curves which can be requested from atom info windows.
Histograms:Ordinate Maximum & Histograms:Sampling Width: Used to display the histograms produced by Batch/Stat/Atom Prms. Changes in the values of ordinate maximum and sampling width can be made dynamically using the keyboard shortcuts ⌘¨, ⌘Æ, ⌘≠ and ⌘Ø.
• Steric Settings...:
Nearest Atom Range (√Ö): Used in Utilities/Look For/Nearest Atoms.
Steric Threshold (kcal): Under this threshold steric conflicts are neglected.
Clash Profile Interpolation (points): Used for the Clash Profile procedure in atom info windows.
Show Clash Between Atoms During Torsion : Clash forecast and display during torsion when a torsion atom has been selected.
• EDmap Settings...: Feature not available on all versions.
Higher/Lower Threshold:
Show ED map frame.
• Atom Parameters Analysis...: Operate structural statistics on .FIT files (up to 104 files) located in the 'Batch Fldr' or on the current structure. Statistics can be done on Bond Length Spread or Bond Angle Spread or Torsion Angle Spread, SS-Bond Angle Spread or H-Bond Angle Spread. However, if a structure is already in memory, the Current structure can be analyzed and statistics will be done with standard deviations. If the Batch button is selected, the results are displayed in a series of stat windows which can be saved on disk. Clicking on one of the bottom marks of a stat window gives the length and angle information. Displaying histograms is possible by clicking on a stat window with the OptionKey down: histogram parameters can be set through the Utilities/StdW Settings menu. Clicking OK in the dialog with the OptionKey down will display all stat windows in the histogram mode.
RamPlot (Ramachandran Plot) of the Current structure or of all Batch files (files located in the Batch Fldr) can also be done; plots including all residues or only/except the selected residues can be done (a multiple selection is possible). Clicking on a point gives phi, psi and name of the corresponding residue (which is shortly highlighted in the current structure). Clicking with the OptionKey down: shows the energy profile of the corresponding residue; move the mouse to see the energy profile changing with psi. 3 cases for the energy profile: Pro, Gly and all the rest. Clicking with the ControlKey down: shows the energy map of the concerned residue; move the mouse to see the local energy; click the mouse to stop.
• Sequence Analysis...: Feature not available on all versions. Operate motif and sequence statistics on .FIT files (up to 104 files) located in the 'Batch Fldr' or on the current structure.
• Select...: Limit display to 1 or More portions of structure in memory. Possibility to select chains. Type highlights only blocks of the selected type. It is also possible to show/hide the differents elements of a structure and to select blocks on the basis of their main chain state, of the Ramachandran region they occupy or of their class (hydrophobic, hydrophillic, positively or negatively charged). Pen settings for the class-based selection are predetermined: yellow (hydrophobic), green (hydrophillic), red (positively charged) and blue (negatively charged)
Subsequent analysis of the structure in memory will only be limited to selected portion(s).
• Write...: Write all data that are available (highlighted): Sequence & Composition, Coordinates, Charges, Occupation & B-Factors, Bond Lengths, Bond Angles, Torsion Angles, H-bonds, I- Bonds, SS-Bonds, Secondary Structures, Steric Conflicts .
Many of these data can only be written if they have been previously looked for (Utilities/Look For).
For Secondary Structures, structural information concerning each residue is given:
region (region of Ramachandran plot): pack (helix region), packG (symetrical of helix region), extd (sheet region), extdG (symetrical of sheet region), out (none of the preceeding);
state : alpha, 310, strand, turn, coil;
phi : phi angle in degree.
psi : psi angle in degree.
chi1 : chi1 angle in degree.
OBded: indicates to what atom(s) main chain oxygen is H-bonded (Bded= bonded).
NBded: indicates to what atom(s) main chain nitrogen is H-bonded.
SCBded: indicates to what atom(s) side chain atoms are H-bonded.
If the OptionKey was down when the Write button was selected, results are written to disk. This is highly recommended when resquests concern H-bonds or secondary structure of big structures.
• Look For:
* Sec-Struct: Determine the secondary structure class of each residue (alpha, 310, strand, turn, coil).
* H-Bonds: Look for H-bonds. 'FoldIt (light)' calculates the missing protons implicated in H-bonds.
* I-Bonds: Look for ionic bonds.
If Sec-Struct/H-Bond/I-Bond menu items have been chosen with the OptionKey down, results will be made automatically visible on the image window.
If Sec-Struct/H-Bond/I-Bond menu items have been chosen with the OptionKey down, results will be made automatically visible on the image window.
* SS-Bonds: Look for SS-bonds (this is automatically done each time a PDB structure is loaded into memory).
* All Sec-Bds: Look for all secondary bonds (H-bonds & I-bonds).
* Steric Conflicts: Determine which atoms are collided with energies above 'Steric Threshold'.
* Near Atoms/Near Residues (item enabled if 1 atom or 1 residue has been selected): Mark and list all atoms or all residues located at a distance < Near Atom Range to the first selected atom or the selected residue; the atoms linked by 3 or less covalent bonds to the selected atom are ignored.
• Overlap:
* Structural: Overlap 2 structures having same length. If called with ControlKey down, identical residues on both structures will be selected.
* Sequential: Feature not available on all versions.
• Tools: Only for development purposes (not available in all versions).
• .PDB=>.FIT...: Transform all '.PDB', '.pdb' or '.ent' files (up to 400!) located in the 'Batch Fldr' into .FIT files, and store them on disk in that same 'Batch Fldr'. As FoldIt is able to work in background, the computer can still be used for other purposes during the .PDB=>.FIT operation. Moreover, if full CPU power is requested for another process for a given period of time, this operation can be paused/reactivated using the File/Pause menu.
Image menu
• Image Settings...: Display mode can be set to Alpha Carbons Only, Main Chain Only, or Main Chain & Side Chain, with or without H-atoms; ⌘M is the keyboard shortcut to swap one mode for the next (the OptionKey reverses the swapping order). There is an option to show side chains of selected residues when the Main Chain Only mode is turned on. The rotation axis can be set through this dialog or by using the ⌘B keyboard shortcut to swap from one axis to the next (the OptionKey reverses the swapping order). Hetero-atoms, water molecules and H-Bonds can be visualized or not. Use ⌘H to show or hide H-bonds. B-Factor Display can be set; Stereo Angle and Motion Speed can be chosen; The information concerning interatomic distances & angles (obtained after clicking on 2,3 or 4 atoms) can be displayed or not ('Show Length & Angle Info' Button).
Stereo Angle can be set dynamically on a stereo image with the help of the two shortcuts ⌘¨ and ⌘Æ (the stereo angle is displayed).
• Pen Settings...: The pen Size, Pattern & Color for all structure elements can be selected. Pen size can be adjusted from 1 to 4 points; pattern can be set to gray, ltgray, dkgray or black; 7 colors can be choosen (this doesn't however apply completely to selected blocks —Selected—): black, yellow, magenta, red, blue, green, cyan, white.
• Animate...: Calculate a number of Frames separated by Increment degrees; these frames are then played back at a Speed (°/sec); an animation sequence can be saved (Animate & Save) and Replay(ed) later. Up to 360 frames (depending only on available memory) can be played.
• Replay a saved animation.
• Stereo: Display a stereo pair of the structure in memory; stereo angle can be set in Image/Image Settings as well as with the help of the ⌘¨ and ⌘Æ shortcuts (the stereo angle is displayed); To displace the stereo pair on the screen use the usual 'Drag with the SpaceBar down' procedure. To modify the distance between both stereo images (or even to interchange them!), drag with the SpaceBar down AND with the OptionKey down (the pixel distance between both structures is displayed).
• Rotate:
Any structure motion can be stopped by pressing any key or the mouse.
* Reset: Bring the Zoom and Rotate conditions to standard setting.
* Right & Left: (‚åòR &‚åòL) Control the direction of rotation (Right=clockwise).
* Wobble (⌘W): Wobble the structure by 20° around the Z-axis (vertical).
* Tumble (‚åòT): Tumble structure around its rotation atom (handy with very small structures).
• Zoom:
Any structure motion can be stop by pressing any key or the mouse.
* Zoom In & Zoom Out: (‚åò+ &‚åò-) Zoom the image around the rotation atom (which doesn't move). The zoom factor is indicated in √Ö/cm in the Report window.
If the zoom operation is performed with the ControlKeyDown, the visible surrounding of the rotation atom will be changed instead of the zoom factor. Releasing keys will stop zooming.
• Recenter: (⌘=) Bring the rotation atom to the center of the Image window. If the rotation atom belongs to a non visible part of the structure, the gravity center of the structure (based on CA atoms) is brought to the center of the Image window. If the OptionKey was down when this menu item was selected, it will bring the rotation atom to the center of the Image window and set the zoom factor to a value which will make the structure as big as possible.
• Swap Mode: (⌘M) Swap the display mode between Side Chain, Main Chain, Backbone. If the Shift key is down, the swap order is reversed.
• Show/Hide H-Bonds: (⌘H) Swap the display mode of H-Bonds.
• Show/Hide I-Bonds: (⌘I) Swap the display mode of I-Bonds.
• Motion StepWise: Decomposes motion (Zoom, Rotate & Turn Bond) into steps; step increment can be set in Image/Image Settings;
• Motion Structure2: (⌘2) Allows motion only of the second structure;
