Simply moving the mouse over a structure will display:
* atom names if the Command or Option key is down,
* block names if the Control key is down,
• SELECTING UTILITY ATOMS WITH THE COMMAND KEY:
If the Command key is down:
* Click once on an atom to define it as a new rotation atom: the whole structure will then be displayed with this rotation atom for center.
* Double click on this atom to define it as a new torsion atom (torsion constraints are ignored); if click occurs too far from any atom, the current torsion atom is deleted. If Utilities/Steric Settings.../Show Clash Between Atoms During Torsion is on, the non covalently bonded clashed atoms are marked as torsion proceeds.
• SELECTING ATOMS WITH THE OPTION KEY:
Clicking once on an atom will select it; clicking twice will call up an atom info window.
* Up to 50 atoms can be selected by simple clicking. Click on the first atom to select it and get its name; As soon as the first atom has been selected, the menu Utilities/Look For/Near Atoms allows you to look for the neighbor atoms. Click on a second atom to get the distance between the two; click on a third atom to get the bond angle formed by these three atoms; and click on a forth atom to get the torsion angle of the third atom. Clicking on an already selected atom will de-select it and will shift down the selection order of the others. If click occurs too far away from any atom, all selected atoms will be de-selected. The length & angle information will be only visible if the dialog setting File/Preferences.../Show Length & Angle Info has been checked.
* Double click on an atom to call up an atom info window; the left column of this window provides some structural information — some of which is editable. The right column of this window gives the names of neighbor atoms as well as the names of atoms forming H-bonds, ionic bonds, SS-bond with this atom or atoms which are in collision with it: this is of course only applicable if H-bonds, ionic bonds, SS-bonds or steric conflicts have been previously founded. Each line has a button which will lead to another atom info window.
The Apply Changes To Structure button executes the changes —if any— which were made in the editable fields; this button can also be activated by the Return or Enter keys.
Atom info windows are modal dialogs: to return to the program, click on Put This Dialog in Background to leave the dialog.
The Top Profile button calls up a Top window i.e. the topological energy curve of the atom; this curve shows the local energetically favored conformations of the set of atoms surrounding the selected atom relatively to the preceding set of atoms. Top profiles are stored in the 'FoldIt Prefs' folder that you should have put in your system folder. Clicking on a Top window with the Option key down swaps the scaling mode.
The Clash Profile button calls up a Clash window i.e. the changes in energy as torsion proceeds around the studied atom. The precision of the calculation can be set through Utilities/Steric Settings/Clash Profile Interpolation.
Clicking the mouse on a Top window or on a Clash window gives the local angle and energy. If the OptionKey is down, clicking and dragging the mouse gives the continuous variation of the angle and energy parameters.
• SELECTING BLOCKS WITH THE CONTROL KEY:
If the option Utilities/Select.../Paint Selected Blocks is on, the selected block will be highlighted. Clicking once on a block will select it; clicking twice will call up a block info window. With the help of the dialog Utilities/Select... it is possible 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).
* Click on an atom to select the residue it belongs to and to see its name; After the first residue has been selected, the menu Utilities/Look For/Near Residues allows looking for the neighbor residues. Clicking on an already selected residue will de-select it. If click occurs too far away from any atom, all residues are de-selected.
* Double click on any atom of a block to call up a block info window showing the class of the residue, its angles phi and psi, and information concerning the H-bond state of its main chain or of its side chain (if H-Bonds have been previously founded).
• A click in a goAway box closes the window definitively except for the Image & Report windows which can be recalled with the Window menu. If the OptionKey is down while clicking in a goAway box, all windows of the same type close.
