Main Menu |
Submenu |
Function |
File |
New
Open
Close |
Create a new untitled document.
Open an RSM script.
Close the current document. |
Save
Save as |
Save the current document.
Save the document as an RSM script.
See RasMol command 'save'. |
Load molec. file |
Open a molecular file under the
chosen format.
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 |
|
Exit |
Exit program. |
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 RasTop specific '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. |
Molecule |
Information
Sequence
Symmetry
Phi psi angles
Ramachandran |
See the RasMol command 'show'. |
Molecular file |
Edit the molecular file. |
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. |
Axes and Boxes |
Unit cell
Axes
Bound box |
See the RasMol parameters 'unit cell', axes, and bound
box. |
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'. |
Measure |
Distance
Angle
Torsion |
See picking mode. |
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 See
the RasMol command 'label' |
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 |
Wireframe
Sticks
Ball and Stick |
Display the selection with a wireframe
Display the selection with sticks
Display the selection as "balls and sticks". |
Bonds See
the RasMol commands 'wireframe'
and 'dash'. |
Display
Remove
Display only |
Display all bonds.
Remove all bond representations.
Display only bonds. |
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. The dot
set is created dynamically at running time by RasTop. |
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 |
Backgrd fade
Stereo
Shadows |
See the RasMol parameter 'backfade'.
See the RasMol parameter 'stereo'.
See the RasMol parameter 'shadow'. |
Slab mode |
Reject
Half
Hollow
Solid
Section |
See the RasMol parameter 'backfade'. |
Autodepth |
Control the display of depthcue vectors in
slab mode. Vectors have a stronger light intensity as they are closer to the front
plan. Deep vectors have a decreased light intensity that makes them sometimes
difficult to see in slab mode. In autodepth mode, the maximum light intensity is set to
the slab plan. |
Main
Toolbar
Select Toolbar
Color Picker
Command Panel
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. |
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. |
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. |