sigle.gif (4112 bytes)

RasTop 1.3. Help
Home | About | Copyrights | Notice | Commands | Programs | Library

dotnul.gif (43 bytes)
Commands:
arrow1.gif (162 bytes)Using RasTop
arrow1.gif (162 bytes)Using RasMol
arrow1.gif (162 bytes)Menu Commands
arrow1.gif (162 bytes)All Commands
arrow1.gif (162 bytes)RasMol Reference
arrow1.gif (162 bytes)Internal Parameters
arrow1.gif (162 bytes)Atom Expression
arrow1.gif (162 bytes)Colour Schemes
arrow1.gif (162 bytes)Atom Sets
Content:
Menu
   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
Menu Shortcuts
Mouse
Molec. File Editing
Main Toolbar
Selection Toolbar
Color Palette
Control Panel
Status Bar
Preferences

Using RasTop

Running RasTop

RasTop is only available on Windows 9x and Windows NT platforms. 

Installing RasTop: Extract the RasTop folder from the rastop.zip file. Install the RasTop folder in the directory of your choice. To get RasTop icon in the start-up manager, proceed as following: 1) Right-click on RasTop.exe and select 'create shortcut'; 2) Transfer the shortcut into the folder "C://Windows/Start Menu/Programs".

To start RasTop, double click on the RasTop icon. When started for the first time, the program displays a single main window and one empty graphic window.

Click under the file>Preferences menu option to activate the Preferences dialog box. Fix the size of the control pannel if necessary. Locate the help source, this site, by browsing your hard-drive and selecting the file "default.html" in the RasTop help folder; URLs are also accepted.

RasTop is a multi-document interface. Several graphic windows, each displaying a single molecular file, can be opened at the same time. Graphic windows are independent from each other, but can communicate using the clipboard to transfer various information such as spatial position and current atom selection. The same molecular file can be opened simultaneously in several graphic windows.

The main window contains the following elements:

- one, or several graphic windows.
- a menu (check menu commands here),
- a main toolbar,
- a selection toolbar,
- a color palette,
- a control panel,
- a status bar,

Most of these elements are switched on and off by clicking in the pull-down menu under 'view' (View>). The size of the control panel can be adjusted in the preferences depending on your graphical unit interface.


Graphic Windows

Graphic windows display a 32-bits output with a maximum of 1024 different colors per window. An 8-bits version is also available, but not distributed. The 8-bits version is available by compiling the source. Note that most export formats are still under their initial 8-bits RasMol version. These routines still need to be updated, and so far the best way to export 32-bits color images is the clipboard (the MAC format PIC seems well supported too!).

Click on the top right of the window menu bar to resize, iconize, or maximize the window. Use the mouse to move, rotate, zoom, or slab the molecule. Left-clik the mouse to obtain information on a particular atom or operate the picking mode.


Menu

Click here to see all menu commands.

With RasMol, most commands are entered manually in a command line window distinct from the graphic window. For exemple you type 'spacefill on' to generate a sphere rendering. RasTop does not require manual entries, but the concept of script commands is still in use, just  in a way that is transparent to the user. In fact most of the menu commands generate their own script that is transferred to RasMol internally. Some operations are more than simple commands. In general, menu commands to manipulate atoms, bonds, and envelops are active, i.e. they activate the rendering. For example coloring bonds in green generates the script commands 'bonds on' and 'color bonds green'. Some commands also keep memory of the last action. For example, if you draw spheres of radius 120, the next sphere command will draw spheres of radius 120. This might be confusing when switching graphic windows, but overall simplifies the rendering operations.

RasTop, as RasMol, supports only one type of envelops, namely dots. RasTop provides an atom set called 'envelop' which contains all atoms currently represented with dots. This set is updated internally each time dots are created or removed. Dot commands apply to all currently selected atoms plus all atoms in the set envelop. To manipulate only dots without creating new one, you must first select the set 'envelop' (see the atom set box).


Menu Shortcuts

To activate a shortcut, press the corresponding letter while maintaining the Ctrl key down.

dotnul.gif (43 bytes)
Ctrl-A      Select All
Ctrl-C      Copy Selection
Ctrl-D      Define
Ctrl-E      Select Expression
Ctrl-F      Full Screen
Ctrl-I      Copy Image
Ctrl-L      Load Molecular File
Ctrl-N      New graphic window
Ctrl-O      Open an <*.rsm> script
Ctrl-P      Print
Ctrl-Q      Select Inverse
Ctrl-R      Restrict
Ctrl-S      Save
Ctrl-T      Tile all graphic windows
Ctrl-V      Paste
Ctrl-W      Show Selection
Ctrl-X      Copy Selection
Ctrl-Z      Select Previous


Mouse

Action Mouse Click
Rotate X,Y Left
Translate X,Y Right
Rotate Z Shift key + Right
Zoom Shift key + Left
Slab Plane Ctrl key + Left
Back Clipping Ctrl key + Right


Molecular File Editing

RasTop supports limited molecular file editing. The molecular file dialog box acts as a simple text editor. Drag the cursor with the mouse left button down to select text areas; use the shortcuts Ctrl-X, Ctrl-C, and Ctrl-V to cut, copy and paste, respectively.

Name box:   Change the name of the current file.

Format box:   Change the current molecular file format.

Export option:   Export the molecular file as a text file.

Process option:   Save the changes to the molecular file and reprocess it. The rendering information are discarded.

Save option:   Save the molecular file, do not process it, and keep the rendering information. To visualize the changes on screen, proceed as following:

1. Save the modified molecular file.
2. Save your work as an <*.rsm> script.
3. Reopen your saved file.

If you save on your previous <*.rsm> file, it is irreversibly modified. It is safer to make modifications of the molecular file on a copy of your <*.rsm> script. To do so, save initially your script under a different name, or reopen your script using the File>Open menu command - it is not possible to open a copy of an <*.rsm> script using the 'most recent file' list at the bottom of the file menu drop-down.

Close option:   Exit the molecular file editing box without saving.


Main Toolbar

main_new.jpg (4226 bytes)    Create a new untitled graphic window. File>New menu shortcut.
main_open.jpg (5944 bytes)    Open an <*.rsm> file. File>Open menu shortcut.
main_save.jpg (5475 bytes)    Save the active graphic window. File>Save menu shortcut.
main_print.jpg (5844 bytes)    Print the active graphic window. File>Print menu shortcut.

main_color.jpg (5126 bytes)    Toggle color palette
main_tile.jpg (5929 bytes)    Tile all graphic windows. View>Tile menu shortcut.
main_molec.jpg (5616 bytes)    Edit the molecular file.


Selection Toolbar

Drag the selection toolbar to obtain a palette:

select_window.GIF (2582 bytes)

selection_all.jpg (4855 bytes)     Select all atoms.  Edit>Select>All menu shortcut.
selection_previous.jpg (6576 bytes)     Go back to the previous selection. Edit>Select>Previous menu shortcut.
selection_inverse.jpg (6436 bytes)     Select the inverse selection. Edit>Select>Inverse menu shortcut.
selection_edit.jpg (6302 bytes)     Select an expression. Edit>Select>Expression menu shortcut.
selection_show.jpg (6726 bytes)     Show the selected atoms. Edit>Select>Show menu shortcut.

 

Atom set box

selection_box.jpg (5794 bytes)

At start, the atom set box contains all atom sets predefined by RasMol and the dynamic set 'envelop', which contains atoms represented with dots. User-defined atom sets are declared at run time using the RasMol command 'define' (Edit>Define menu shortcut). New identifiers are added at the bottom of the drop-down list as new sets are created. The atoms currently selected in the molecule are modulated by the selected atom set by clicking one of the following icons:

selection_new.jpg (5624 bytes)    Select atom set, discard current selection.
selection_add.jpg (6359 bytes)    Add atom set to current selection.
selection_remove.jpg (5696 bytes)    Remove atoms in common with current selection.
selection_extract.jpg (5580 bytes)    Select atoms in common with current selection.
selection_exclude.jpg (5624 bytes)    Exclude current selection from atom set.

Note that atom sets defined at run time are saved in the RSM script format.

Picking mode

The picking mode is activated by clicking once a picking icon and deactivated either by clicking the same icon again, or by clicking twice in the window screen anywhere. Deactivating the picking mode updates the previous selection set stored in memory; unless, the previous selection refers to the initial atom selection.

By default, clicking an atom displays its residue name, residue number, atom name, atom serial number and chain in the information line, see RasMol 'picking ident' parameter. Pressing the Ctrl key while clicking switches the display to atom coordinates.

Picking Icons:

picking_atom.jpg (3945 bytes)    Select an atom. Pressing the Shift key together adds the atom to the current selection, pressing the Ctrl key removes it. Dragging the mouse while maintaining the left mouse button down will generates a squared lasso on screen. All atoms in the square will be selected on mouse up. The Shift key and the Ctrl key control the lasso selection as well. The lasso effect is better visible in the 'show selection' view mode.  To rotate the molecule with the mouse, bring the cursor to the border of the window until the picking cursor disappears. Left click the mouse and drag the mouse.

picking_group.jpg (5723 bytes)    Select a group (a residue). Use Shift key and Ctrl Key to modulate the selection.

picking_chain.jpg (5250 bytes)    Select a chain. Use Shift key and Ctrl Key to modulate the selection.

picking_bonds.jpg (4035 bytes)    Display a double bond when single bonded atoms are clicked consecutively, or a triple bond for a double bond, respectively. Adding one bond to a triple sends back to a single bond; pressing the Ctrl key together adds two bonds or remove one by circular permutation. Multiple bonds cannot be saved, nor drawn from a RasMol script. Alternatively, multiple bonds can be written in the molecular file, for example by repeating the bond declaration in pdb files.

picking_center.jpg (5291 bytes)    Move the center to the clicked atom. If the Ctrl key is pressed together, the center is further moved to the center of the screen.

picking_label.jpg (4870 bytes)    Add or remove labels.

picking_monitor.jpg (4022 bytes)    Add monitors. See the RasMol parameter 'picking'.

picking_distance.jpg (4596 bytes)picking_angle.jpg (4847 bytes)picking_torsion.jpg (4757 bytes)    Measure distances, angles, or torsions, respectively; see the RasMol parameter 'picking'.


Color Palette

color_palette.GIF (2973 bytes)The drop-down menu lists the different RasMol elements. Click any color icon to fill them with color. See details in the RasMol command 'colour'. The icon labeled with a <+> activates a Windows color picker; the <-> label corresponds to the command 'color none', i.e. the elements take the color of the supporting atoms. Note that not all elements support the none color.

 


Control Panel

The size of the control panel is adjusted in the preferences. Do so if the control pannel appears very small or too large on your screen.

From left to right:

Rotate check box:   When checked, command the three interactive scrollbars to rotate the molecule along the x, y, or z axis, respectively.

Translate check box:   When checked, command the three interactive scrollbars to translate the molecule in the x or y plane, or to zoom the molecule.

Reset button:   Restore the original viewing transformation and centre of rotation. See the RasMol command 'reset'.

Auto button:   Rotate automatically the molecule. Clicking in the left or the right cursor of the scrollbars adjusts the rotation speed and axe.

Slab cursor:   Adjust slab plane in slab mode. See RasMol command 'slab'. Dragging the cursor to the left margin turns off the slab mode; see the RasMol command 'slab off'.

Depth cursor:   Adjust back-clipping plane. See RasMol command 'depth'.

Light cursor:   Adjust ambient lighting. See the RasMol parameter 'ambient'.

Specular cursor:   Adjust specpower. See RasMol parameters 'specpower' and 'specular'.

Shade cursor:   Adjust shadepower. See RasTop parameter 'shadepower'.

Information line:  Display varied information, comments, or warnings generated by RasMol or by RasTop.  Right-click the mouse to copy its content.

Status light:   Take different colors according to RasTop status.

Light Grey:   Standby or RasTop ongoing operation.

Dark blue:   Ongoing calculation by "RasMol molecular engine."

Yellow:       Same as light grey, but a script is running.

Orange:      Pause in a script. Press any key to continue the script or the Esc key to interrupt the script.

Red:           Lost focus. The script keeps paused even when pressing keys.  Click once in the graphic window to get the input focus; then press any key or Esc to interrupt the script.

Dark blue lighting replaces the waiting cursor in RasMol. If RasTop does not respond, but the status light if dark, it means that the program is probably engaged in a time-consuming operation such as file loading or calculation of a molecular transformation.


Status bar

Relay some help information, in particular from the menu and the command panel. Toggle off in View>Status Bar menu command.


Preferences

Zoom factor: The zoom factor is an enlargement factor applied to images copied to the clipboard. A value of 2 often improves image resolution. Factors above 4 generate large, if not huge, image files and must be used with caution. Using a high image resolution may decrease the size of some objects; adjust the dot size and draw bonds as cylinders if necessary. Be aware that using a graphical output such as a printer or a screen at a resolution lower than the resolution of your graphic file may impair image quality.
Mouse binding: Only RasMol binding is available.
     
Panel size: Adjust the size of the command panel if necessary. Check "Large panel" is the command panel appears too small on the screen.
Sequence output: One letter or three letters code output for the molecule>sequence menu command.
Help source: Indicate where RasTop will find the help site when activating the help>help RasTop menu command.

The first time you start RasTop, the help source points to the directory 'C:\'. Browse your directory and select the file 'default.html' in the folder help located in the rastop folder.  URLs (http:\\www...) are also accepted.

 

dotnul.gif (43 bytes)
RasTop Help - home | notice | copyright
(c) CopyRight Philippe Valadon © 2000