Chapter 8 View Menu
This menu contains the following commands:
Control Panel Brings up a dialog box to scale, translate and rotate structures in the structure window.
Labels Brings up a dialog box to change the structure labels
Mono/Stereo Toggles between mono and stereo display
Stick Figure Display all structures as stick figures.
Ball and Stick Display all structures as Shaded ball and stick figures.
Pluto Display all structures as Pluto type ball and stick figures.
Tubular Bonds Display all structures with tubular bonds.
CPK Surface Display all or selected structures with CPK surface.
Dot Surface Display all or selected structures with dot surface.
Ribbon Display a Ribbon diagram of peptide or nucleic acid backbone
RedGreen Stereo Toggles red/green stereo display.
Top View Turns on/off a top view of the current structure
Dipole Moment Draws a dipole moment along with structure.
Selecting CONTROL_PANEL brings up a dialog box containing seven controls which allow scaling, translation and rotation of the current molecular system.
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The SCALE control allows the structure to be reduced or enlarged. Enlarging the structure is useful when trying to select atoms in congested systems, and reducing the structure can be useful when visualizing large structures.
The three TRANSLATE controls move the molecular system in the X, Y, or Z directions. The X direction is horizontal on the screen, the Y direction is vertical, and the Z direction is perpendicular to the screen.
The three ROTATE controls rotate the system around the respective axes.
RESET_VIEW returns the molecular system to the coordinates it had when the CONTROL_PANEL option was selected. All translations and rotations are reset, but changes in scale remain in effect.
RESET_SCALE resets the scale size to the default value. It has no effect on rotations or translations.
EXIT dismisses the dialog box.
To move one substructure relative to other substructures, use the MOVE command under the SUBSTR menu.
Selecting LABELS brings up a dialog box through which the currently displayed labels can be changed. The default is to only show bonds. Clicking on "OK" will close this window, with the selected display type enabled, and this display type will be remembered and made the default when you exit PCMODEL..
The options are:
Hydrogrens and lone pairs - places the letter "H" at each hydrogen position, and displays lone pairs as a pair of dots. This does not add hydrogens or lone pairs, it only displays them if they exist.
Bonds only (default) - removes all atom symbols from the display, but atoms and bonds are shown in their normal colors. This is especially useful with large structures which quickly become cluttered when atom symbols are displayed.
Atom numbers - labels each atom with its individual atom number. This is useful for setting up files for GMMX, the global searching program, which works on atom numbers. It is also useful when trying to interpret output given in terms of atom numbers.
MMX Atom Types - labels each atom with its MMX atom type number. This is useful for examining parameters used in the MMX calculations, since these are given by atom type. (see Chapter 7 for a complete list of atom types and the corresponding numbers).
MM3 Atom Types - labels each atom with its MM3 atom type number. This is useful for examining parameters used in the MM3 calculations, since these are given by atom type in the file MM3.PRM.
MMFF94 Atom Types - labels each atom with its MMFF94 atom type number. This is useful for examining parameters used in the MMFF94 calculations, since these are given by atom type in the file MMFF94.PRM.
AMBER Atom Types - labels each atom with its Amber atom type number. This is useful for examining parameters used in the Amber calculations, since these are given by atom type in the file AMBER.PRM.
Oplsaa Atom Types - labels each atom with its Oplsaa atom type number. This is useful for examining parameters used in the Oplsaa calculations, since these are given by atom type in the file OPLSAA.PRM.
Atomic Charge - labels each atom with its current atomic charge. This will be zero (0.0) until a calculation is done, and the charges will be specific to the force field used in the calculation.
Substructure number - labels each atom with a number representing its substructure membership. This number is a value form 0 to 255 and is the sum of 2substructure number for all substructures for which the atom is a member.
Color by substructure - colors the bonds by the lowest substructure number at each atom.
Color by Strain - During a calculation the energy for each interaction is partitioned by atom. The individual atomic energy components are then normalized and colors are assigned to each atom based on the magnitude of the energy with Red being the most energetic, followed by rose, yellow, green, cyan, magenta, blue and gray.
This option changes the default display between one structure (Mono) and two structures displayed side by side in stereo. The stereo display can be rotated inward or outward, though the use of STEREO option in the OPTIONS menu. In stereo mode the two structures are rotated + and - three degrees from the mono structure to simulate a stereographic display.
Selecting this option returns the current drawing mode to the default stick figure display of all atoms.
Selecting this option displays the current structure with small balls representing the atoms and tubular bonds connecting the atoms.
Selecting this option displays the current structure as a Pluto type ball and stick figure with shading.
Selecting this option displays the current structure with thick bonds.
This option displays the current molecular system as a CPK model
This option displays the current molecular system with a dot surface around it.
This option draws a ribbon for the backbone of a peptide or nucleic acid chain. The display can be of the ribbon only, or the ribbon and a stick representation of the structure itself. The type of molecule (acyclic protein, cyclic protein or DNA/RNA) must be indicated.
The dialog box offers a choice of Oxygen-Oxygen (default) or swapped orientation of the ribbon. Oxygen-oxygen produces smooth ribbons for alpha helices, while swapped produces smooth ribbons for sheets.
The algorithm searches for the first N-terminus and draws the ribbon from there. Once it cannot find another amide linkage in the chain, it stops there and draws the ribbon. The ribbon display remains in effect until either the STICK_FIGURE option is selected or the Ribbon dialog box is brought up and canceled. The ribbon display can be rotated and translated, and can be printed.
Redraws the current structure in stick figure form using red and green images to create a stereo image when viewed through red/green glasses.
Draws a second view of the current structure rotated by 90 degrees. The top view is smaller and placed in the upper or lower corner, but this allows two views of the same structure simultaneously.
Draws a vector representing the computed dipole moment of the current structure. The dipole vector will be rotated with the current structure.