Some of these commands are very commonly used, others are not frequently used. Some are part of the pull-down menu system, pothers could be made part of the user's .menu system.
The next identified atom becomes the screen centre. Atoms can be identified by picking at the screen or by using the Terminal_id command.
terminal_id <mol res atom> <object>
Identify an atom by typing on the terminal. This command is normally used in macros.The program prompts for the atom and then the object name.
Ignore any command until an ID is made. This command is used exclusively in macros. The ID must be made by picking an atom.
This commands stops the current work session. The database is saved to the file specified in the datablock 'file_O_save', as if the command Save_DB was activated.
Stop the work session withour saving. The <ESC> key accoplishes this too.
Set the Yes flag on, the No flag off. This command is a 'utility' command, and is being used by several other commands. When input from this command, or its friend, No is required, a prompt is shown in the message area of the display. For example:
Hit *Yes to accept, *No to cancel.
Great care must be taken if multiple commands are active that wait for a Yes or No. They will be affected in the order that appears in the active command line of the display. The leftmost command will receive the Yes or No.
Set the No flag on, the Yes flag off. See the description of Yes.
Clear all flags. This command cancels all active commands. If atomic coordinates are being changed, e.g. by Lego_side_chain, the command issues a No.
Save the O database in a previously assigned file. The first time the command is activated, the user is prompted to decide the file where the database is to be written. The name of this file is stored in the database in the text datablock 'file_O_save' and can be changed using the distributed macros @change_save_file or @save_as. As distributed, this macro activates an editor 'edt'. The Save_DB command should be activated every time you have made any important modifications in the database!
Remove ID text from all molecular objects.
Macros @change_save_file.macro or @save_as to change the name of the file in which the user's data base is stored is supplied with the O distribution.
File_O_save: a text data block storing the file name of the user's data base.
Menu <major_menu_name or text> <on/off> <colour>
Control what menus are displayed and therefore visible to the user on the display. If the text is a major menu, all commands for that menu are put onto the screen. To add the Lego commands to the screen, for example, just do
O > menu lego ;;
To add a macro called map, do
O > menu @map ;
The new commands are added to the bottom of the menu.
A list of available major menus can be obtained by typing
O > menu ?
The screen menu is maintained in a datablock called .menu and can be changed in other ways. For example, its contents can be converted in a formatted file with Write_formatted , edited with your favourite editor-remembering to correctly update the number of lines, and then added back into the database with Read_formatted command.
symbol name <text string>
Adds a symbol definition to the program. The name of the symbol must not include a $ character. To use the symbol, the user adds a $ to the start of the symbol name. For example,
O> symbol greetings "Hullo world"
O> print $greetings
O> Hullo world
The terminal line is parsed and any set of characters representing a current symbol is replaced by the symbol expansion. Symbols are particularly useful with macros to define which molecule or map to work with, for example. To remove a symbol, run the command with prompting and hit a <CR> instead of a new text string.
1.Control of echoing commands on the terminal that come from indirect files.
2.Control logging of command line input to a file 'o_log.fmt' . This is useful to create templates for macros.
3.Control logging of terminal listing to a file 'o_log.lst'. This option can be used to keep track of the output from complicated operations, such as the lsq commands. The listings of O output in this manual were created using this option.
Spawn another process in the operating system. In Unix, the shell is closed by logout, exit, or <CTRL>-D if this option is enabled in your shell environment.
Issue a one line shell command to the operating system.
Toggle Stereo on and off . We use the crystal eyes stereo system. This splits the video memory for a left and right eye image with a loss of resolution in the vertical direction.Stereo can also be activated by the F1 keys . On some machines, thje styereo implementation can result in overlapping opened terminal windows. These can be avoided by using a smaller window, positioned at the lower left hand corner of the screen
rot_tran_obj <transformation> <object>
Rotate / translate a 3D graphical object (normally not a molecule object but for use with maps, 'rsc_db', or 'ca_db'). The object must exist. It could be created by the user (e.g. with the Map_draw or Draw_object commands) or by program options with defined names (Lego_ca creates an objects 'ca_db' and 'ala_db', while Lego_side creates an object 'rsc_db'). In the object list that may be drawn on the screen, the transformed objects have '_rt' appended to its name. <transformation> is a datablock in the database containing the rotation and translation operators. It must be
the complete name e.g. .lsq_rt_a_to_b
centre_atom <mol residue atom>
Define the '.active_centre' by typing an atom name. The user can type molecule residue and atom explicitly or defaults as specific atom in a particular molecule. The coordinate is taken as orthogonal Ångstrøm's.
centre_xyz <x y z>
Define the '.active_centre' by a entering a coordinate value at the terminal.
Backup the user Database to another disk file. The name of the backup file is stored in the text datablock File_O_Backup.
message "Hi you guys"
Send a message to be displayed on the screen. Use in your macros to say what you are doing.
draw_object <data_block_name>
Add a new object to those being displayed. The user specifies a text block in the database that contains drawing instructions in the O graphics descriptor format (see Chapter 7, 'General Drawing Instructions').
When several dial sets are active at the same time, this command can be used to cycle between them in a forward direction. For example, the Move_fragment command activates two dial sets, one for the rotations around the x, y, z axes, and one for the translations. Dial_next will select the next dial set on the stack. This command changes this assignment by one block of four, cycling through 4 dial boxes. For each box number, there must be an entry in the database .box<number> Default examples are included in odat/dialbox.o, dialbox_a.o and in the odat/startup.o files.
This command functions equivalently to Dial_next, but cycles in the opposite direction through 4 dial box settings
dial_box <number>
This command allows one to explicitly define which dialbox is to be mapped to the dials. A search of the data base for .box<number> is made and a mapping made between the logical input device numbers and the 8 dials.
For example, if one wishes to control all of the rotations and translations for a moving fragment and have the zoom and slab active on the same box, one may use a box number 5 and have in the data base an entry
.box5 i 8 (3i3)
9 10 11 4 13 14 15 8
rotate_picture <axis> <angle>
Apply a rotation about one of the screen axes. Specify the axis and the angle. Can be used for taking stereopictures, if the rotation angle is 6°, e.g.
rot_pic y 6.
screen_colour <colour>
Set the colour of the screen background. This is useful when taking pictures of solids.
et the view spinning automatically for a while. Mainly for testing purposes. Spins through 100 views.
Print a message on the terminal. Used in macros.
Ring a bell on the terminal. Used in macros to wake up the user.
if_yes_no <macro1> <macro2>
This command allows one to do a very simple if type statement. The first macro will be activated if YES is set, the second one if NO is set.
centre_zone <id two atoms> or <mol res1 res2>
The picture centre is redefined as the centre of gravity of the defined zone
centre_next <property> <operator> <value>
Move to the next atom or residue along the sequence that fullfill the criteria of the logical expression. A sister command, Centre_prev, moves in the backward direction. Examples:
centre_next atom_name = ca
sets the current active centre at next C-alpha position.
centre_next residue_type = lys
centres on next lysine residue.
centre_next residue_rsfit < 0.8
Centres on next residue with a rsfit correlation coefficient worse than 0.8
centre_prev <property> <operator> <value>
Same as Centre_next, but moves backwards in the sequence.