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| Commands:
Using RasTop Menu Summary References. Internal Parameters
Atom Expression
Colour Schemes
Atom Sets
RasTop World

RasTop Menu Commands

File Edit Molecule Atoms Bonds | Ribbons Envelops View Window Help

| Main Menu | Submenus | Function
--- | --- | --- | ---
| File | New Open Add Close | Create a new untitled document. Open RSM scripts, "pdb" and "cif" files. Add an RSM script to the current world, see '`add`' command Close the current document.
Save Save as Save Mol. as | Save the current document if modified. Save the document as an RSM script, see command '`save`'. Save the active molecule as an RSM script.
Load mol. file | Load a molecular file into the current world, see the RasMol command '`load`'. Depending on the status of the connect mode, the connectivity information is loaded or ignored.
Load script | See RasMol '`script`' command. Most scripts have the extension <*.src>, main scripts have sometimes the extension <*.top>.
Export | Image Molecular file Script data | See the RasMol '`write`' command. See the RasMol '`save`' command. See the RasMol '`write script`' command. To export images, use export 'bmp' or 'pict' commands or use the clipboard. The export 'gif' menu works only with the 8-bit version.
Print Print setup | Print the current view. If the view is larger than the page, the image is resized.
Preferences | See Preferences.
Exit | Exit program.
| Edit | Copy | Image | Copy a bipmap file to the clipboard. The image can now be pasted in other software. See also preferences for the zoom factor.
Selection Position | Copy the current atom selection or the spatial position to the clipboard. See specific clipboard formats and the '`copy`' command.
Paste |  | Paste the current atom selection or spatial position from the clipboard. See specific clipboard formats and the RasTop specific '`paste`' command.
Select | All Inverse Previous | Select all atoms. Inverse the current selection. Return to the previous selection. If the picking mode is on, return to the initial selection.
Expression Within | See the RasMol '`select`' command. See the RasMol '`select within`' command.
| Show | Show the current selection on screen. See RasMol parameter '`display`'.
Edit | Atoms Groups Chains Coordinates | Edit atoms, groups, chains, or atom coordinates of the current selection as a text file that can be exported.
Pick | Atoms Groups Chains Center | See picking mode. This is better done on the main toolbar.
Mode | Internal Bonds Hydrogens Heteroatoms Models | See the parameter '`bond modes and/or`' See the internal parameter '`hydrogen`'. See the internal parameter '`hetero`'. Control the selection of atoms when several models are opened. If '`models`' is on, atom selection will occur in all models simultaneously.
Define | See the RasMol command '`define`', and the atom set box.
Restrict | See the RasMol command '`restrict`'.
Command | Open a dialog box to enter RasMol script command manually.
| Molecule | Delete Molec. | Delete the active molecule, see '`zap molecule`' command .
Information | Molecule World Atom Selection Group Selection Chain Selection
Coordinates
See the command '`show`'.
Sequence | See the RasMol command '`show`'.
Molecular file | Edit the molecular file.
Symmetry Phi psi angles Ramachandran | See the RasMol command '`show`'.
Hide or Show | Hide or show the active molecule, see '`molecule`' command.
Structure | Calculate Renumber Connect Cis angle | See the RasMol command '`structure`'. See the RasMol command '`renumber`'. See the RasMol command '`connect`'. See the RasMol parameter '`cis angle`'.
Connect Mode | See the RasMol command '`connect`'. If the connect mode is false when loading a molecular file, RasTop uses the connectivity information of the input file.
Monitors | Add/Remove Remove all Show values | Add and remove monitors, see picking mode. See the RasMol command '`monitor off`'. See the RasMol parameter '`monitor`'.
Axes & Boxes | Unit cell Bound box Axes World Axes | See the RasMol parameters '`unit cell`', '`bound box``'`, and`'axes'`.
Centre See the command '`centre`' | Selection World Origin Origin to centre Centre to origin | Center to selected atoms Center world to center of canvas Center to world origin Transfer world origin to current center. Transfer current center to world origin. Molecules are translated.
Rotate | See the RasMol command 'rotate'.
| Atoms | Spacefill See the RasMol commands '`spacefill`' and '`star`'. | Display Remove Display only | Display spacefill in the current selection. Remove spacefill from the current selection Display only spacefill in the selection.
Sphere Star | Spacefilling using spheres. Spacefilling using stars.
Fixed Radius Van der Waals Temperature User | Radius of fixed value. Van der Waals radius. Radius according to temperature User defined radius.
Labels | Display Remove Pick | Display labels on all selected atoms. Remove labels from all selected atoms. See picking mode.
residues | Label each selected group.
Format | Format the labeling. See the RasMol parameters '`font stroke`' and '`fontsize`'.
Color | CPK Shapely Structure Group Chain
Temperature
Charge
User
Model
Alternate
Color the spacefilling.
See the RasMol command '`colour`'.
Atom color controls the color of labels, monitors, bonds and ribbonds when the none color is selected for these elements, see color palette.
| Bonds | Bonds See the RasMol commands 'wireframe' and 'dash'. | Display Remove Display only | Display all bonds. Remove all bond representations. Display only bonds.
Reset | Reset bonds, see '`reset`' command.
Type | Wire Dash Cylinder | Display bonds with wires. Display bonds with dashed lines. Display bonds with cylinders.
Mode | None Not bonded All | Control the spacefill representation of single atoms that are not bonded. See the RasMol parameter 'set bondmode'.
Multiple bonds | Add/Remove Show | See picking mode. Activate or disable multiple bonds representation.
H bonds See the RasMol command '`Hbonds`. | Display Remove | Display selected H bonds Remove selected H bonds.
Type | Dash Cylinder | Control representation.
Mode | Sidechain Backbone | Control binding to backbone. See the RasMol parameter '`Hbonds`'.
Color | Type | See the RasMol parameter '`color Hbonds`'.
SS bonds See the RasMol command '`SSbonds`. | Display Remove | Display selected SS bonds Remove selected SS bonds.
Type | Dash Cylinder | Control representation.
Mode | Sidechain Backbone | Control binding to backbone. See the RasMol parameter '`SSbonds`'.
| Ribbons | Display Remove Display only | Display, remove, or display only a ribbon representation in the current selection. The ribbon mode is chosen among the five following options: '`ribbons`', `'strands`', `'cartoon`', '`trace`, and '`backbone`'. Different from RasMol, the backbone representation cannot be displayed simultaneously with an other ribbon representation. Nevertheless, this is accomplished by entering the scripting information manually.
Ribbons Strands Cartoons Trace Backbone | Set the current ribbon representation. See the RasMol commands '`ribbons`', `'strands`', `'cartoon`', '`trace`', and '`backbone`'.
Settings | Beta arrows Dash Dots Height Radius
Strand number
Structure
Temperature
Width
Wire
Possible options are highlighted according to the possibilities of the current ribbon representation.

See the RasMol command '`set cartoon`', `ribbons`', `strands`', `cartoon`, '`trace`', and '`backbone`'.

| Envelops | Display dots Remove dots | Display or remove dots in the current selection. See the RasMol command '`dots`'. To select all dots, i.e. all atoms represented with dots, select the dot envelop in the atom sets box and click the adjacent "new" icon.
Van der Waals Conolly | Control the display of a van der Waals or a solvent accessible surface around the currently selected set of atoms. See the RasMol parameters '`radius`' and '`solvent`'.
Dot size Radius size Dot density | See the RasMol parameter '`dot <value>`'. See the RasMol parameter '`radius`'. See the RasMol command '`dots <value>`'.
Potential | See the RasMol colour scheme on potential.
| View | Light Source Backgrd fade | See the RasMol parameter '`set headlight`'. See the RasMol parameter '`backfade`'.
Stereo Stereo Angle | See the RasMol parameter '`stereo`'.
Shadows | See the RasMol parameter '`shadow`'. Not active in version 2.0
Reset Depth | See the RasMol parameters '`depth`' and '`reset`'.
Reset Slab | See the RasMol parameters '`slab`' and '`reset`'.
Slab Mode | Reject Half Hollow Solid Section | See the RasMol parameter '`slabmode`'.
| Window | Tile Tile Horizontal Tile Vertical Cascade Arrange | Tile all graphic windows with a length/width ratio close to unity. Tile all graphic windows horizontally. Tile all graphic windows vertically. Cascade all graphic windows. Arrange iconic graphic windows.
Main Toolbar Select Toolbar Color Picker Command Pan. Status Bar | Toggle the main toolbar. Toggle the selection toolbar. Toggle the color picker. Toggle the command panel. Toggle the status bar.
Full screen | Toggle all visible toolbars together.
| Help | Help RasTop | Start your default browser and open this site. The location of the RasTop Help Site must be entered in the preferences to activate this command.

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