REMARK COIL ATOM ... ... ATOM ... REMARK BETA-STRAND ATOM ... ... ATOM ... REMARK COIL ATOM ... ... ATOM ... REMARK ALPHA-HELIX ATOM ... ...PDB files generated by the program will follow this convention to preserve secondary structures information.
The program tries to be as lenient as possible when parsing a given PDB file. Comments will reliably be ignored, but HETATM lines can sometimes cause trouble. In case of doubt, those lines should be removed manually.
Conf: 999999999999999999999999999999999999999 Pred: CCEEEEEEEECCCEEEEEEEECCHHHHHHCCCCEEEECC AA: GGGMMMLLTTSPSAAAVVAAILLAMATISPSTRMMLLGGThe first line defines prediction confidence values ranging from zero to nine (not used by the current program version). The second line defines predicted structures: "C" stands for coil region, "E" stands for beta-strand, and "H" stands for alpha-helix. The third line defines residue types using the standard PDB single letter residue names.
When reading a prediction file, the program will automatically add an ACE residue at the beginning of the protein, and an NME residue at the end. Both residues will be of residue type "Unknown," and will not be affected by any protein manipulations. They will, however, be included in any PDB file written by the program.
Clicking and dragging with the middle mouse button will pan the display parallel to the viewing plane.
Clicking and dragging up and down with both the left and middle mouse button will dolly out from and in towards the current view center, respectively.
Pressing the "z" hotkey, and subsequently picking any atom with the left mouse button will move the view center to the picked atom.
The view can be reset to show the entire protein by selecting the "Center View" entry from the "View" menu, or by pressing the "Alt-c" hotkey.
Residue Selection
Residues inside the manipulated protein can be selected in one of two ways: Either by clicking on one of the residue's atoms with the left mouse button while holding down the "Alt" key, or by dragging the "Residue index" slider inside the Residue Dialog. The selected residue will be highlighted by rendering its atoms.
The Residue Dialog displays information about the selected residue, and can also be used to randomly assign dihedral angles for coil residues by selecting the "Random Angles" button.
Structure Selection
Secondary structures inside the manipulated protein can be selected in two ways: Either by clicking on one of the structure's atoms with the left mouse button while holding down the "Ctrl" key, or by dragging the "Structure index" slider inside the Structure Dialog. The selected structure will be highlighted by surrounding it with a green semi-transparent box. This box doubles as the main 3D interaction widget for aligning secondary structures.
The Structure Dialog displays information about the selected structure, and can also be used to globally manipulate the dihedral angles of all residues inside alpha-helices or beta-strands.
Any structure manipulation will only change dihedral angles of rotatable backbone bonds. Bond distances or angles will never be changed; neither will peptide bond dihedral angles or phi angles of proline residues.
Structure Alignment
To align secondary structures, the program provides a 3D direct manipulation widget that can be translated and rotated using the mouse. By selecting a secondary structure, it will be enclosed in a semi-transparent green box, and the next coil region towards the beginning or end of the manipulated protein (depending on the current update direction) will become the current update region (highlighted by rendering its backbone (ribbon) in yellow). Any manipulations of the green box will be translated into dihedral angle changes inside the update region, and the program will update the protein atoms' cartesian coordinates interactively.
To manipulate the drag box, a user picks it with the left mouse button while holding down the "Shift" key. Depending on which part of the box was picked, it can subsequently be manipulated in one of three ways:
Tip: Sometimes it is helpful to "wiggle" the box a bit during manipulation to help the program find a vector of dihedral angles that approximates the goal orientation well.
For the purposes of undoing/redoing, a complete dragging motion, between mouse button push and mouse button release, will count as an atomic manipulation.
Changing the Update Direction
When a secondary structure is selected, one of its neighbouring coil regions becomes the current update region (which is subsequently affected by manipulating the green box surrounding the selected structure). The update region is found by traversing the protein either to the left or right, i.e., towards the ACE initial or the NME terminal) until the next coil region is encountered. The update direction, i.e., the direction in which the protein is traversed, can be toggled by pressing the "u" hotkey. When the update direction is changed, the new update region is determined immediately and highlighted by rendering its backbone (ribbon) in yellow.
Beta-Strand Adjustment
Structure alignment will only change dihedral angles inside coil regions, but never inside alpha-helices or beta-strands. To change the shape of beta-strands, the program supports adjusting four parameters for each beta-strand independently. Each parameter has a corresponding roller widget inside the Structure Dialog.
If a feature has an assigned hotkey, pressing the hotkey by itself will toggle the global setting, whereas pressing the hotkey while holding down the "Ctrl" key will toggle the per-structure setting.
Atom Rendering
When Atom Rendering is enabled, all atoms of a secondary structure will be rendered as colored shaded spheres. Sphere radii are defined as the respective atoms' van der Waals radii, as taken from A. Bondi, "van der Waals Volumes and Radii", J. Phys. Chem. 68 (1964), pp. 441-451.
This feature can be toggled via the Drawing Toggles Dialog, or via the "a" hotkey.
Sidechain Bond Rendering
This feature renders bonds between all atoms as shaded capped cylinders. The cylinders are colored based on the element types of the two atoms involved in a bond. This feature is useful to get an idea of side chain alignment, and to track down atom intersections when used in combination with the Atom Collision Visualization feature.
This feature can be toggled via the Drawing Toggles Dialog, or via the "b" hotkey.
Backbone Ribbon Rendering
This feature renders a protein's backbone as a single colored shaded spline ribbon. When disabled, the protein's backbone is simply rendered as a colored polyline. The backbone colors are assigned according to secondary structure type: Alpha-helices are colored red-purple, beta-strands are colored blue-purple, and coil regions are colored plain purple.
This feature can be toggled via the Drawing Toggles Dialog, or via the "r" hotkey.
Hydrogen Bond Rendering
This feature renders hydrogen bonds between backbone dipole groups (N-H and C=O) as dotted yellow lines. The decision of when to form hydrogen bonds is based on the distances between two involved dipole groups, and on the angle between their respective bonds. The geometry constraints determining whether two opposite dipole groups will form a hydrogen bond were taken from the main-chain hydrogen bonding histograms on the web page Atlas of Side-Chain and Main-Chain Hydrogen Bonding by Ian McDonald and Janet M. Thornton.
This feature can be toggled via the Drawing Toggles Dialog, or via the "h" hotkey. Hydrogen bond rendering can only be toggled globally, so there is no per-structure toggle button and no "Ctrl-h" hotkey.
Hydrogen Bond Site Rendering
This feature is meant to assist in aligning beta-strands into beta-sheets. It renders backbone dipole groups as colored lines (light blue for N-H, red for C=O). The lines are extrapolated such that they extend half the distance of an average hydrogen bond past their group's minor atom (H and O, respectively). The endpoint of the extended line is also marked by a dot. In effect, to form a "prototypical" hydrogen bond, a user has to align one blue and red line each to be anti-parallel, and overlay their end dots.
This hydrogen bond guide is less precise than Hydrogen Cage Rendering, but it introduces less clutter.
This feature can be toggled via the Drawing Toggles Dialog, or via the "s" hotkey. Since hydrogen bond sites are mostly used to create beta-sheets, they are by default only enabled for beta-strands.
Hydrogen Cage Rendering
This feature aids in aligning beta-strands by displaying hydrogen bond regions around N-H dipole groups. When enabled, it will draw dark-yellow wireframe cages around the valid region for the oxygen atom of a backbone C=O dipole group, and will highlight C=O groups by red lines and dots at the oxygen atom's position. When an oxygen atom is inside this region, and the hydrogen bond angle constraint is satisfied, a hydrogen bond can be formed.
This feature can be toggled via the Drawing Toggles Dialog, or via the "c" hotkey. Since hydrogen cages are mostly used to create beta-sheets, they are by default only enabled for beta-strands.
Large vs. Small Hydrogen Cages
To reduce clutter when drawing hydrogen cages, one can disable rendering of the "inner" shell of the cages.
This feature can be toggled via the Drawing Toggles Dialog, or via the "Ctrl-l" hotkey. Hydrogen cage size can only be toggled per structure, so there is no global toggle button and no "l" hotkey.
Atom Collision Visualization
This feature aids in aligning structures and creating overall protein conformations. When enabled, it will visualize intersecting atoms inside a protein as red shaded spheres of varying radii. When determining intersections, the program considers all N2 pairs of atoms. Even though a spatial data structure is used to reduce collision detection complexity to expected O(N), enabling this feature will slow down interaction and rendering.
Two atoms are considered intersecting if and only if their Euclidean distance is less than 75% of the sum of their respective covalent radii, as taken from http://www.webelements.com. The sphere visualizing an atom intersection is centered at the geometric midpoint of the two affected atoms, and its radius is calculated as the difference of 75% of the sum of covalent radii and the Euclidean atom distance, multiplied by two. In other words, the radius of an intersection sphere is twice the intersection depth.
This feature can be toggled via the Drawing Toggles Dialog, or via the "p" hotkey. Atom collision visualization can only be toggled globally, so there is no per-structure toggle button and no "Ctrl-p" hotkey.
Figure 1: Residue Dialog (a) No residue selected. (b) Residue selected.
The rest of the dialog is only enabled when a residue is selected. The "Residue type" field displays the selected residue's type, and the "PDB file name" field displays the residue's name from the PDB file/prediction file.
The fields inside the "Dihedral Angles" group display the residue's current dihedral angles phi and psi in degrees. Selecting the "Randomize Angles" button will assign random dihedral angles for a residue inside a coil region.
Structure Dialog
Figure 2: Structure Dialog (a) No secondary structure selected. (b) Alpha-helix selected. (c) Beta-strand selected.
The rest of the dialog is only enabled when a secondary structure is selected. The "Structure Type" field displays the selected structure's type (coil, alpha-helix or beta-strand).
The rollers and buttons inside the "Beta Strand Shape Adjustment" group are used to adjust a selected beta-strand's shape.
Drawing Toggles Dialog
Figure 3: Drawing Toggles Dialog (a) No secondary structure selected. (b) Secondary structure selected.