These are the essential commands that a user needs to know about in O. Here I introduce the most important commands, in the order you are likely to need to know about them. I also describe some other things that will help a new user get started.
| Getting started | how to start working after loading the distribution |
| Pull-downs | explains the pull-down menu system |
| Mouse, F keys, esc, ctrl | explains how to use the mouse, Function keys and 2 other special keys to control the program |
| PDB | these are the standard input and output coordinate files to O, although the program can read other ones too (WAH, RD ....) |
| Molecular line objects | generate various types of line objects from molecules in the program's database. |
| Control | there are a large group of instructions that can be classified as control commands, e.g. Save, yes, no .... |
| Customizing | the user's environment can be customized in a number of ways |
| Using macros | macros greatly extend O's capabilities |
| Contouring | the F(ast)m(ap) electron density real-time contouring and fitting commands |
| Grab | the commands that allow you to move atoms around by pointing with the mouse. |
| Flip 'n tor | another set of commands to rebuild a molecule |
| Regularize | the commands that allow you to restore standard geometry, after introducing distortions. |
| Skeletons | used to help trace a structure in an electron density map. |
| Colouring | colour is used in lots of places in O; the interface, molecular objects, contoured density .... |
| Protein databases | main-chain and side-chain databases are available for building protein molecule |
| Trig. info. | provides tools to calculate various trignometric information(distances, angles, contacts, phi/psi, h-bonds....) |
| Symmetry | generates crystallographic symmetry objects from a molecule |
| Comparing molecules | commands to compare molecules and display the results of the comparison. |
| Mutate | mutate a molecule, replace, insert, delete residues |
| Sketch | make quality solid sketches |
| Plot | generate a plot meta file for use with oplot |
| Notes | make 3D notes to remind you what the density is telling you |
Once the distribution has been ftp'ed from Uppsala, there should be a few directories that have been created on the home computer system. Two directories are absolute requirements, a third one is to be recomended. The installation must have a directory containing the program, normally called the o/bin directory. If the installation is to a DEC Unix workstation, for example, the user would create an alias to the most recent experimental version of the program, using something like
% alias axp_o /usr/people/o/bin/axp_sauron
where the person responsible for installing the program, has created a directory /usr/people/o/bin for holding the executables.
The installation must also have a directory containing some of the information that O works with, e.g. the files desribing the latest menu, databases etc. This directory is best reached when running O by using the Unix environment paramaters. If the directory is /usr/people/o/data this can be achieved by the following
% setenv ODAT /usr/people/o/data
One usefull thing about this Unix command is that one can define more paths to this variable. For example, one could point to the local PDB, O macros .....
% setenv ODAT $ODAT:/home/joe/o/macros
and when running O, the program would check for the files in the relevent ditrectories.
Now you are ready to start the program. If you do not have your own O file, you would just do the following, hitting <return> until a black 3D window appears
% axp_o
....
If the program issues a warning that some commands have been disabled, the user does not have access codes for the workstation. These are stored in the data directory, in the access.o file. If codes have not been issued, contact alwyn@xray.bmc.uu.se . If they have been issued, there is something wrong with the local access.o file which should be in the data directory.
The third directory contains examples. It is recommended the new user starts by working with these and some of the documentation provided elsewhere. Make yourself your own working directory, and copy all of the files from the example directory into yours. Then start by typing
% axp_o p2.o menu.o access.o
and hit a bunch of <returns>. This forces the reading of the local versions of the menu.o and access.o files are included to ensure that the most recent version of the menu is being used, as welll as the local version of the .access datablock. The order is important. Now you can do the introduction to O exercises.
O functions are activated by keywords, pull-down menus or macros containing a group of keywords. Most keywords take the form of sam_atom_in ,for example. This commands is activated if the user types sam_at_in or s_a_i or numerous other possibilities. What is typed must be sufficient to recognize the keyword. So typing just sam_atom would not be enough since there is also a command sam_atom_out. Many keywords require data input, and again O gives the user some flexibility in how to enter this information. If just the keyword is entered (either at the 3D window, or at the X-terminal window), the user will be prompted for the extra data. If the user knows what data is to be entered, it can be typed on the same line as the keyword. e.g.
O > s_a_i 1crn.pdb 1crn
will read in the coordinates of crambin and give the molecule the name 1crn.
Multiple keywords and /or data can be on the same line, e.g.
O > s_a_i 1crn.pdb 1crn mol 1crn ca ; end
is enough to read in crambin, make and display an object of just the CA atoms. The ';' in the above line indicates to the O-parser that the user would hit a <return> if prompted, and would be the equivalent of accepting the default (in this case a zone describing all the molecule). Special care must be taken with the input of text where buried spaces are allowed. Such input can be delimited by double quote characters (").
The parser recognizes 4 special characters, @, !, # and $. The '@' character before a keyword specifies a macro file of commands. All characters following a '!' on a line are treated as comments. The special character, '#', is mainly used in macros. The character string between a pair of #'s will be written to the terminal and be replaced by whatever is typed at the terminal. This allows macros to prompt for terminal input. A word starting with a $ is recognised as a symbol and will be expanded by the parser. For example, the macro draw_mol contains the following commands
% cat draw_mol
! macro to draw a sphere of atoms of user defined radius
mol $my_mol centre_atom a131 c1
spher #'Define sphere radius#'
end_object
It would be activated in O by typing
O > @draw_mol
and would make an object of all atoms within a sphere centred on a particualr atom of a particular residue (the radius defined by the user at run time) for the molecule defined by the symbol my_mol.
Mouse and Function Keys in O 6.x (980216)
The mouse right button when depressed, in the 3D window, controls the view. Moving the mouse rotates the picture in the direction of the motion. To rotate the view alround a vertical axis, slide the mouse to the right or left. To rotate around a horizontal axis, slide the mouse up or down.
Depressing the right and middle buttons at the same time, rotates the picture around the third axis, perpendicular to the scree. Moving the mouse down rotates the picture clockwise, and moving it up rotates it anti-clockwise.
The middle buton when depressed by itself, controls both zoom and clipping. Up down for zoom, and right-left for clipping.
The left key is used for identifying atoms and activating the windowing system.
The action of right and middle mouse buttons may, in some circumstances, be affected by depressing certain 'special' keys. For users who do not have dials, the mouse can be used with the Ctrl-key. In O, four dials are always assigned to control of the view. These are not matched to mouse equivalents, since something like them already exists. The other four dials are assigned on the fly to whatever commands may be active. The actual affect of turing a dial depends on which logical dial box has been assigned to the four dials. These can be changed by the Dial_last, Dial_next commands. The mappings to the four dials are
dial 5 - ctrl, right mouse horizontal motion
dial 6 - ctrl, right mouse vertical motion
dial 7 - ctrl, middle and right mouse vertical motion
dial 8 - ctrl, middle mouse vertical motion
The following function keys are used:
F1 - controls stereo on/off i if supported by the hardware.
F2 - controls text (menus, prompts etc) on/off
F3 - changes a line drawing mode. When solids and lines are to be drawn, the mode has to be changed to get the correct 3D affect.
F11 - is only used on SG machines. Those with old versions of OpenGL must hit this key to get the correct 3D affect.
F12 - prints on the keyboard the present function key settings.
The keyboard <esc> key quits the program without saving the contents of the user's database
The keyboard <ctrl> key is used in the Grab commands to apply rotations to the grabbed atoms. If the workstation has no dials, the user can use a mapping of the dial box via the ctrl-key and mouse button combinations. BUT ....
If the user moves the mouse outside the 3D window when ctrl is pressed, and then the key is released, and then the mouse moved back into the window, O thinks that the ctrl is still depressed and acts accordingly. Just press ctrl again, and release it.
O reads a number of external cooridnate formats using the Sam_atom_in command. The only format that is widely used today is the Protein Data Bank format. If the coordinates file type ends in .pdb , O will assume this is the format and then prompt for a 5 letter molecule name.The program saves various information that might be in the file, including cell constants, space group name etc. It does NOT store anisotropic temperature factors. Files with unexpected endings are prompted for the coordinate type.
O supports writing out a number of different coordinate formats using the Sam_atom_out command. Only the PDB type is widely used today. The user can write out just those that are selected, if he/she so wishes. The program decides on which format to write out by recognizing the file type. For PDB style coordinates the type should be .pdb If the type is not recognized, the program prompts for the file type.
The usefullness of O can be greatly extended by the judicious use of macros. These are groups of instructions that may be freqently used. By putting them in a macro, just activating the macro starts processing the contents of the list.
The O line parser recognises a macro by the special character '@'. Macros can be in the computer's local file system or as part of the user's database. When the parser identifies a macro, it first tries to open it as part of the file system ,then as an entry in the user's database.
Consider the macro that is automatically activated when O starts. It has the name on_startup. If it is part of the file system it may look like this
% cat on_startup
window_open user_menu .8 .8
window_open object_menu -1.1 -0.1
fm_file ano1.map mir
If part of the user's database, it would be a text data-block entry as follow
@on_startup t 3 50
window_open user_menu .8 .8
window_open object_menu -1.1 -0.1
fm_file ano1.map mir
If the macro contains a wait_id command, processing of the macro will be stopped until the user identifies an atom