Running the Program.

To run the program, set the directory to example/ and then type (user input in boldface) something like the following (it will, of course, depend on your machine type) :

 
%  cd o/example 
%  ../bin/es_ono_5.9 
O> Use of this program implies acceptance of conditions
O> described in Appendix 1 of the O manual
O> O version 5.9, August 1993
O> Define an O file (terminate with blank) : p2.o  
O> Define an O file (terminate with blank) :
O> Maximum inter-residue link distance = 2.00
O> There were 23 residues.
O>           175 atoms.
O>

or simply

 
%../bin/es_ono_5.9 p2.o
O > Use of this program implies acceptance of conditions
O > described in Appendix 1 of the O manual
O > O version 5.9, August 1993
O > Maximum inter-residue link distance = 2.00
O > There were 23 residues.
O >           175 atoms.
O > Do you want to use the display ? [Y],N :
O >

After a delay, you should see a 3-D window, plus menu and prompt areas. The 3-D window shows a CA drawing of P2 myelin and a fatty acid. Move the mouse to the command On_off and click any button. The names of the currently displayed objects will appear. Click them on and off. To make a larger object for timing purposes, move the mouse over the terminal window and enter the following commands:

obj all z ; end

To make the picture spin, just type the command Spin. It will update 100 times, changing by 3.6 degrees each time. To get a map, type the macro @map_a. Edit the file to increase the volume of density being displayed (in line 3, it defines a cube of 12Å). Now read the manual and look at the examples provided.