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Main
Menu |
Submenus |
Function |
|
File |
New
Open
Close |
Create a new untitled
document.
Open RSM scripts, and
(RasTop 1.3.1) "pdb" and "cif" files.
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. |