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RasTop 2.0 Help
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  Commands:
arrow1.gif (162 bytes)Using RasTop
arrow1.gif (162 bytes)RasTop World
arrow1.gif (162 bytes)Menu
arrow1.gif (162 bytes)Summary
arrow1.gif (162 bytes)References.
arrow1.gif (162 bytes)Internal Parameters
arrow1.gif (162 bytes)Atom Expression
arrow1.gif (162 bytes)Colour Schemes
arrow1.gif (162 bytes)Atom Sets

RasTop Menu Commands

arrow1.gif (162 bytes)File
arrow1.gif (162 bytes)Edit
arrow1.gif (162 bytes)Molecule
arrow1.gif (162 bytes)Atoms 
arrow1.gif (162 bytes)Bonds
arrow1.gif (162 bytes)Ribbons
arrow1.gif (162 bytes)Envelops
arrow1.gif (162 bytes)View
arrow1.gif (162 bytes)Window
arrow1.gif (162 bytes)Help

up.gif (912 bytes) Main Menu Submenus Function
up.gif (912 bytes) 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.
Note that the most formats to export image files are not supported in the 32-bits version. The clipboard is often a simpler method.
Print
Print setup
Print the current view. If the view is larger than the page, the image is resized.
Preferences
Load Prefs
See Preferences.
Load a new preference file
Exit Exit program.
up.gif (912 bytes) Edit Copy Image Copy a bipmap file <*.bmp> to the clipboard. 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.
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.
up.gif (912 bytes) 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'.
up.gif (912 bytes) 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.
up.gif (912 bytes) 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'.
up.gif (912 bytes) 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'.

up.gif (912 bytes) 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.
up.gif (912 bytes) 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'.
up.gif (912 bytes) 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.
up.gif (912 bytes) 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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RasTop Help Site - home | notice | copyright
(c) CopyRight Philippe Valadon 2000-2001
All publishing rights reserved. 
Last updated on Sunday, January 13, 2002