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RasTop 1.3. Help
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Using RasTop Running RasTopRasTop 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:
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 WindowsGraphic 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. MenuClick 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 ShortcutsTo activate a shortcut, press the corresponding letter while maintaining the Ctrl key down.
Mouse
Molecular File EditingRasTop 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
Selection ToolbarDrag the selection toolbar to obtain a palette:
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:
Note that atom sets defined at run time are saved in the RSM script format. 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:
Color Palette
Control PanelThe 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.
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 barRelay some help information, in particular from the menu and the command panel. Toggle off in View>Status Bar menu command. Preferences
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Using RasTop
Create a new untitled graphic window. 
Open an <*.rsm> file. 
Save the active graphic window. 
Print the active graphic window. 
Toggle 
Tile all graphic windows. 
Edit the 
Select all atoms. 
Go back to the previous selection. 
Select the inverse selection. 
Select an 
Show the selected atoms. 
Select atom set, 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.
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 '
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.
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.
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.
Add or remove labels.
Add monitors. See the RasMol parameter '
Measure distances, angles, or torsions, respectively; see the RasMol
parameter '
The drop-down menu lists the
different RasMol elements. Click any color icon to fill them with color. See details in
the RasMol command '