This menu contains the following commands:
Labels: Brings up a dialog box to change the structure labels
Stick: Display all bonds as sticks..
Tubes: Display all bonds as tubes
Ball and Stick: Display all atoms as balls and bonds as tubes
CPK Surface: Display all atoms as large balls representing a CPK surface.
VDW Surface: Display the VDW surface as a mesh or transparent solid.
BackBone: Display the C alpha carbons of a protein connected with a tubular bond
Ribbon: Display a Ribbon diagram of peptide backbone
Side by Side Stereo: Display the current structure as two images, side by side, rotated
RedGreen Stereo: Displays the current structure with a red/green stereo display.
Dipole Moment: Draws a dipole moment along with structure.
Properties: Displays the properties of the current structure in the Template window.
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 saved and made the default when you exit PCMODEL..
The options are:
Bonds(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 Symbols – displays the atomic symbol for elements except carbon.
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. (mmxconst.prm)
MM3 Atom Types - labels each atom with its MM3 atom type number. (mm3.prm)
MMFF94 Atom Types - labels each atom with its MMFF94 atom type number. (mmff93.prm)
Oplsaa Atom Types - labels each atom with its Oplsaa atom type number. (oplsaa.prm)
United Atom Types ; labels each atom with the type used in the United Atom Force field (oplsua.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.
Molecule number - labels each atom with a number of the molecule to which it belongs. The default is zero.
Substructure - renders each molecule a different color.
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.
The first three drawing options (Stick, Tubes and Ball and Stick) are grouped together and only one can be active at any time. Selecting one turns the other two off.
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 thick bonds.
Selecting this option displays the current structure with small balls representing the atoms and tubular bonds connecting the atoms.
This option displays the current molecular system as a CPK model. It is a quick model that uses spheres set to the vdw radius of each atom type. It it s toggle – select it once to turn it on, select it again to turn it off.
This option is used to display various surface representations of the molecule. A dialog appears in the Templates Window and the options include:
Color By: Nothing (all atoms the same), Atom (each atom is colored with its' standard color), Charge
Resolution: Set the fineness of the grid used in evaluating the surface
Isovalue: The value to plot
Radio buttons to chose the type of display: Mesh or Solid Surface.
The initial calculation of the surface is slow but once rendered the surface can be rotated and translated easily..
This option is a toggle.
These options draw a ribbon or a tubular line for the backbone of a peptide. The display can be of the ribbon and/or back bond only, or the ribbon and/or back bone and a stick,tube or ball and stick representation of the structure itself. (To see the ribbon or back bone only turn off the current stick/tube/ball and stick option but selecting the current option).
These options are both Toggles.
This option changes the default display between one structure (Mono) and two structures displayed side by side in stereo. In stereo mode the two structures are rotated + and - three degrees from the mono structure to simulate a stereographic display.
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 vector representing the computed dipole moment of the current structure. The dipole vector will be rotated with the current structure.
Properties
This option brings up a dialog in the Template Window that list the Name, Molecular Formula, Weight, Number of Atoms, QM energy (if known), MM energy (if known), the MM Force Field used to compute the MM energy, Heat of Formation, Dipole Moment, Dipole Vector, XlogP and whether there is MO or IR data associated with the current structure.