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| Commands:
Using RasTop Menu Summary Reference Internal Parameters
Atom Expression
Colour Schemes
Atom Sets
RasTop World
Content:
Menu Shortcuts Mouse Molec. File Editing Main Toolbar Selection Toolbar
Script Toolbar
Color Palette
Control Panel
Status Bar
Preferences

Installing & Using RasTop

### Getting Started

RasTop is available on Windows and Linux platforms. Linux users should install Wine prior to RasTop. Mac users can use Virtual PC, but it is not free software.

Standard Installation:

Extract the RasTop folder from the rastop.zip file. Install the folder in the directory of your choice. Create a shorcut and place it in a convenient location such as the Desktop.

To start RasTop, double click on the RasTop icon. When started for the first time, the program displays a single main window with one empty graphic window, the color window, and the command line window. Dispose the color window and the command line window on your screen or turn them off.

Preferences are set by default and does not need to be changed at that time.

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 or current atom selection. The same molecular file can be opened simultaneously in different graphic windows or on the same one.

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,
> - a command line.

Most of these elements are switched on and off by clicking in the pull-down menu under 'windows' (Windows>).

Custom Installation:

If your monitor only supports 256 colors, download the rastop8bit.zip file, unzip and replace the original, 32 bit, exe file - RasTop.exe - by the new exe file. Change the name back to RasTop.exe if you wish.

If you cannot get started and always receive the warning message "missing mfc42.dll", download and unzip the patch mfc42.zip; install the file mfc42.dll in the folder containing the RasTop.exe file.

### Tutorial

The chapter is still at its embryonic development stage.

The subfolder "data" in RasTop folder contains a few samples of molecular files. To open your first molecule, click on the menu command file>open. Browse your directories up to the RasTop folder, open successively the folders data and molecule, select a pdb file (a file ending by the extension ".pdb"). A molecule will appear on your screen.

Play with the mouse on screen to move and rotate the molecule. With the left and the right button and with or without the Shift key or the Ctrl key depressed, many options are available.

The file>open menu command also opens RSM scripts, i.e scripted files that contain both molecular and rendering information. This command tolerates direct opening of pbd files and cif files. Other molecular files should be opened using the command file>load molecular file.

To open your first RSM file, click on the menu command file>open. Browse your directories up to the RasTop folder, open successively the folders data and rsm, select the file 2H1.rsm. The antibody 2H1 in complex with the peptide PA1 will appear on screen.

To modulate the rendering, play with the submenu commands under the menus atom, bonds, or ribbons.

Rendering command usually act on selected atoms only. To see the atoms currently selected, click the toolbar button "show selection": . Selected atoms will appear in orange, non-selected atoms will be in dark blue. At this stage all atoms should be selected.

Atom selection is a difficult aspects of molecular rendering. Use the selection toolbar to proceed to varied atom selections. For example, select the word "aromatic" is the pulldown of the property box (located in the selection toolbar) and click on the button "new selection" in the toolbar. All the amino acids of aromatic type are now selected, check by clicking the button "show selection". The amino acid classification used by RasMol is depicted in the amino acid table.

In the original RasMol program written by Roger Sayle, all commands are entered by hand on a command line. In RasTop, the process is the same except that commands are now generated internally. In our example, clicking the "new selection" button generated the command "select aromatic". RasMol script command may be entered manually using the dialog box activated by the menu Edit>Command or more directly at the command line.

Scripting of atom selections is explained in the page atom expression. Complex expressions not available in the menu have to be entered manually after clicking the Edit>Command menu. New users and beginners will take advantage of reading the significance of the commands in the Command Reference page. It is not unusual to enter atom selections by hand.

Starting version 2.0, RasTop can load multiple molecules in a unique "world". An RSM script is added to the current world by the command File>Add, other molecular files are added by a simple File>Load command. When the world cursor is on, all molecules are moved together and when the world cursor if off, only the active molecule is moved. By active molecule, we mean the molecule that is currently selected for rendering. To determine which molecule is the active one, click the toolbar button "show selection": , the non-active molecules are drawn in green whereas the active one is in orange for the selected atoms or in blue for the non-selected atoms. To toggle easily from one view to another, press on the TAB key.

When only one molecule is loaded, it is always better to have the world cursor activated ("world on").

### Graphic Windows

Graphic windows display a 32-bits output with a maximum of 1024 different colors per window. The high color resolution allows 64 shade variations per color. The 8-bits version displays only 256 colors and is adapted to 256 colors monitors. 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.

All commands can be entered manually in the command line window distinct from the graphic window. For example you type '`spacefill on`' to generate a sphere rendering. RasTop does not require manual entries, but the concept of script command 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 between graphic windows, but overall it simplifies the rendering operations.

### Menu Shortcuts

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

> 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-M | Enter RasMol Command
> 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

Pressing the Space key activates or deactivates the Display mode and shows the selected atoms. Edit>Select>Show menu shortcut.

### Mouse

`Action` | `Mouse Click`
--- | ---
`Rotate X,Y` | `Left`
`Translate X,Y` | `Right`
`Rotate Z` | `Shift key + Right Wheel`
`Zoom` | `Shift key + Left Shift or Ctrl key + Wheel`
`World Zoom (Z-translation)` | `Left + Right`
`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 title of the current file.

Format box: Change the molecular file format. The molecular file format must match the format to load successfully.

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. Not available starting version 2.0., indeed save the file and reload it immediately.

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.

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

### Main Toolbar

Create a new untitled graphic window. File>New menu shortcut.
Open an <*.rsm> file. File>Open menu shortcut.
Save the active graphic window. File>Save menu shortcut.
Print the active graphic window. File>Print menu shortcut.
Help
Tile all graphic windows. View>Tile menu shortcut.
Edit the molecular file.

Render selection with CPK spheres.
Render selection with stars
Render selection with wireframe
Render selection with balls & sticks
Remove sphere, star, cylinder, and ribbon rendering

Render selection with ribbon.
Create dot envelop.

Picking mode

The picking mode is activated by clicking a picking icon once 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.

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:

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.

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

Select a chain. Use Shift key and Ctrl Key to modulate the selection.

Select a molecule as active. This option works only when multiple molecules are loaded.

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.

Select or modify bonds. Pressing the Shift key together increase the bond order (create a single bond, single to double bond, double bond to triple bond); inversely pressing the Ctrl key decreases the bond order or delete the bond. The bond created or modified is selected for bond rotation.

Rotate a selected bond. The world must be in off mode (see World check box in control panel) otherwise all molecules rotates around the world origin instead of the selected bond.

Add monitors. See the RasMol parameter '`picking`'.

Add or remove labels.

Measure distances, angles, or torsions, respectively; see the RasMol parameter '`picking`'.

### Selection Toolbar

Change coordinate system from molecular to world and absolute coordinates successively.
Toggle world axes on and off.
Toggle color palette.
Show the selected atoms. Edit>Select>Show menu shortcut.

Select all atoms. Edit>Select>All menu shortcut.
Go back to the previous selection. Edit>Select>Previous menu shortcut.
Select the inverse selection. Edit>Select>Inverse menu shortcut.
Select an expression. Edit>Select>Expression menu shortcut.

Selection boxes:

There are three selection boxes: the element box, the property box, and the user set box. The element box is dedicated to single elements such as carbon or oxygen and predefined set of atoms such as rna or dna; the property concerns atom or group property such as hydrophobic or aromatic amino acids. The user set box contains user-defined atom sets that 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 last element selected in one of the three boxes modifies the current selection using 5 basic operation:

Create new atom selection, discard current selection.
Add atom set to current selection.
Remove atoms in common with current selection.
Select atoms in common with current selection.
Exclude current selection from atom set.

### Scripting Toolbar

Allow a default script to be run after a molecule is loaded; on by default.
The default script can be changed in the Preferences.
Toggle on and off the command line window
Echo RasTop internal commands to the command line.
Useful to learn how RasTop functions and to learn scripting.

Select to run the corresponding script. Scripts are located in the rastop/script folder. Add your own scripts in that folder.

### Command Line

Type in or commands and execute online. The command line accepts common copy and paste function. Change the text color and the background color in the Preferences.

### Color Palette

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

From left to right:

World check box: When checked (" world on") all loaded molecules rotate and move together. This is the default setting even when only one molecule is loaded. Uncheck only when you want to adjust a molecule position in a multiple molecule environment (see the command '`rotate all`'.

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. When the world is active, the zooming effect is centered in the middle of the canvas, otherwise the rotation center is used.

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

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

DepthCue button: Activate depth queuing for spheres, cylinders, and ribbons. See the RasMol command '`set depthcue`'.

Slab button: Switch on and off the slab. See the RasMol command 'slab'.

Slab cursor: Adjust slab plane in slab mode. See RasMol command 'slab'. The value indicated in the buddy window depends of the coordinate system in use.

Depth button: Switch on and off the back-clipping plane. See the RasMol command '`depth`'.

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`'. Note that the range has changed starting version 2.0, and RSM file made with previous version may display a wrong setting.

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

Display information regarding the current atom pointed by the cursor. Toggle off in View>Status Bar menu command. The active coordinate system is indicated in the right end panel.

### Preferences

Starting version 2.0, user preferences are stored in a script file named 'rasmolprefs' located in the folder "C:/Documents and settings/yourname". A second preference file is located in the folder "rastop/lib" and is used to localize RasTop, e.g. to set the default langage.

Clipboard factor: | The clipboard factor is an enlargement factor applied to images copied to the clipboard. A value of 2 usually improves image resolution. Factors above 4 generate large 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.
Sequence output: | One letter or three letters code output for the molecule>sequence menu command.
Coordinate System | Clip plane values and atom coordinates depend of the chosen system.
Default Representation | Indicate a script file that runs automatically after a molecular file is loaded. The first time you start RasTop, the software use a file named default.scr located in the "rastop/script" folder..
Help source: | Indicate where RasTop will find this web site when activating the help>help RasTop menu command. The first time you start RasTop, the software look into "rastop/help" folder for the file index.htm.

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