RasTop Manual |
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Installing & Using RasTop Getting StartedRasTop 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:
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.
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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 | |
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.
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 |
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.
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.
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'.
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.
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.
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.
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.
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.
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.
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.
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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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