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O General Description

The O Home Page has much information. Look at the "Getting Started with O" link.

The Online Manual is available for version 5.10. This has a section called An O Tutorial which is helpful.

Alwyn Jones has an O Essentials command summary. (For O Version 7)

Morten Kjeldgaard has a tutorial on Getting Started with O.

An HTML version of O for Morons is available.

Documentation for most of the Uppsala Software Factory programs from Gerard Kleywegt is available. This link also has much useful information on macros, dictionaries, and tutorials for O.

HOW TO display O images with a white background and other imaging tricks from Mark Harris. (Note: We have GIMP installed in the CSB for these tricks).

NT version of O has been installed on Mason and Yoko in the Core.
On Mason, to launch the program click on the 'Ono-mono' or 'Ono-Stereo' icon on the desktop.
Press F1 to turn off the stereo after launching the Ono-Stereo.

On Yoko to use O follow the instructions.

Here are the site-specific commands to get you started .

In a directory of your choice type the following:

       setup ono (or source /srv/local/setup/ono.set)


Keep the UNIX window with the O> prompt open on the side of the graphics screen to enter commands.

To slow the mouse down, type what is in bold:
O>dir *.dial_real
Heap> .DIAL_REAL R W 1
O>write .DIAL_REAL
Heap> Name of file to be created: tmp.dial
Heap> Format:[return]
(Edit tmp.dial and change the 1.00000 to 0.20000)
O>read tmp.dial

Or do the following:

read /srv/local/ono/omac/dial_speed_sgi.odb

This will create a couple of macros on your menu list that can be used to slow the dials down.

The refi_zone command may be used after the following setup (Thanks to Poul Nissen):

read /srv/local/ono/data/refi_aa_na.o (Need only be read in once - will be saved in the binary)
refi_init [molecule]
refi_generate [molecule]
refi_zone (Click on residues or specify on command line)

Note: Newer versions of O need to re-read the "old-style" access database. To load an existing ".o" file for the first time: After specifying your ".o" file, when the program next says, " Define an O file (terminate with a blank): enter "/srv/local/ono/access.odb" After the file is saved again, the above should not be necessary.

Reference for O:

T.A. Jones, J-Y. Zou, S.W. Cowan and M. Kjeldgaard (1991), Improved methods for the building of protein models in electron density maps and the location of errors in these models. Acta Cryst. A47 110-119.

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Last Modified: Friday, 11-Jul-2003 10:00:22 EDT by P. Fleming