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RasTop 1.3.1 Help
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Using RasTop Getting StartedRasTop is available on Windows 9x, Windows NT, and Windows 2000 platforms. No major problem have been reported so far on Windows ME. Standard Installation: Extract the RasTop folder from the rastop.zip file. Install the folder in the directory of your choice. To get RasTop icon in the start-up manager on Windows 9x platforms, proceed as following: 1) Right-click on RasTop.exe fie 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 panel if necessary. Locate the help source - this site, either by browsing the hard-drive and selecting the file "default.html" in the RasTop help folder, or by manually entering its URL (http://www...) if available (no available at this 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. 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. Custom Installation: If your monitor only supports 256 colors, download the rastop8bit.zip file from the openrasmol site, 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 from the openrasmol site; install the file mfc42.dll in the folder containing the RasTop.exe file. TutorialThe 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 be displayed 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 is in fact reserved for opening 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 with many different rendering effects. To modulate the rendering, play with the submenus command 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": Atom selection is by far one of the most difficult aspect of molecular rendering. Use the selection toolbar to proceed to varied atom selections. For example, select the word "aromatic" is the pulldown of the atom set 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 by type 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". Scripting of atom selections is explained in the page atom expression. Complex expressions not available in the menu can be entered manually by clicking the Edit>Command menu. All the script commands described in this manual can be entered this way. Although it will be the exception execpt for entering specific atom expressions, new users and beginners will take advantage of reading the significance of the command they use in the Command Reference page. 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 example 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 panel 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 center 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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