O

O is installed in /home/bio/O (on garm)
/usr/local/o7.0 (on tjaste)

To run O (version 8), you have to include in .profile
export ODAT=/home/bio/O/data
and in your .alias
alias O="/home/bio/O/bin/lin_ono"
Then you can run o by typing O.
At present, we have licences only for two mashines: loke and balder (Ulf's and Kristina's CPUs).

On tjaste you instead do (vesion 7.0):
export ODAT= /home/local/o7.0/data
alias O="/home/local/o7.0/bin/sg_ov701"

Mapman
is available from:
/home/bio/Bin/Linux/mapman

How to use O

• Start O by typing O
• Press return until you get a window (six times)
• s <cr> gives all commands starting with s
• To read in a pdb file and show it:

s-a-i (sam-atoms-in)
enter pdb file
give it a name (max 5 characters)
mol <name> obj <name1> z[one] ; end (note the blank before ",")
Sometimes, you must also do (on the screen):
Menus - Objects - Select object
before the protein appears on the screen
you may also need to reduce the size of the picture by draging the middle mouse pointer down (because the program centres the picture on the origin, no on the centre of coordinates)
 
• There are four different ways to select which atoms to display (alternatives to zone):
• z[one] <res1> <res2>

shows residues res1-res2
z ;  gives the whole protein (all residues are default)
z 800  - shows only residue 800
• ca[-zone] <res1> <res2>

shows only the CA atoms of each residue from res1 to res2
• cov[er_sphere] <residue atom> <radius>

shows all atoms in all residues within radius from the selected atom (or residue)
• sph[ere_centre) <radius>

shows all atoms within radius from the active centre (selected earlier by ce[ntre]-a[tom])
• All these commands can be combined and several similar commands can be given.

They must all end with the command
end[_object]
before anything is shown
• Controls - Center on atom - Select with the left mouse button

or
ce[nter]-a[tom] <residue number> <atom>
• Control - clear text
• To colour a certain residue:
  pa[int]-pro[perty] res[idue]_typ[e] = phe blue z ; end
  or
  paint-property residue_name < a16 red z ; end
• To colour a protein by atoms:
  @paint_by_atom_type
  or
  pa[int]-ca[se] ato[m]_z 4 6 7 8 16 white blue red green  z ; end
  pa-ca ato_z 4 6 7 8 16 white blue red green  z ; end
• Display - paint molecule - Colour; Disp - Paint molecule - Object
• $ -> gives a unix shell;
• e.g. $ ls (note the blank after $!)
• least square - explicit

lsq-exp
define molecules
give the zone; e.g. a215 a221
save with a name
• lsq-mol

read in the operation
mol <name> obj <name1> z[one]; end
• menu - dist-def on
• Rebuild - Trig - Neightbour atom (~3.2 Å)
• Plot_on

Plot_off
Record a macro
• Display sketch molecule - sketch

Sticks - broader lines
• Ribbons gives better pictures, also with maps
• The best way to make pictures is to use snapshot (unix command)
• stop (ends the program)

The mouse

• Select with the left mouse button
• Rotate with right mouse button
• Zoom with the central mouse button up/down
• Slab with the central mouse button left/right
• Move by pressing Ctrl and the right mouse button

Maps

• They are constructed by CNS, command model_map.inp
• Set upper resolution to 20 Å (not 500 Å)
• Typical maps are u=2 v=1 and u=1 v=1; 3fo-2fc
• Map grid 0.25 (not 0.33 Å)
• Remove real-space R factor
• Remove Water pick
• Remove Fourier coefficient
• The maps can be compressed by mapman

 

 
 
 

• In O
• s-a-i

enter pdb file
give it a name (max 5 chars)
mol <name> obj <name1> z ; end
• fm-f[ile] (fast map)

Enter file name
Density - Click in the box - then the map appears
2fofc level 1
• Maximum 4 maps
• fm-set

2 levels
+3
green
-3
red
• Map-cover

Residue R-factor

• Construct a map with CNS as described above
• construct the rsfit.o file (see below)
• Run the protram mapman to convert the map from cns format to o (brix) format
• re m1 <name_of_the_map_file>
  cns
• br m1 <new_name_of_map>
• quit
• Start O with O  + 6 <cr>
• s-a-i <pdb_file>
• give a name
• mol <name> obj <name1> z[one]; end
• ce-a <atom>
• read rsfit.o (see below)
• rs_fit <residue1> <residue2>
• enter the name of the omap file
• The parameters of rs_fit can be modified by the command 
  rsr_setup
• The map file can be changed by 
  rsr_map

The rsfit.o file should contain one record for each residue of the type:
rsfit_MMP             T         10        70
CHA CHB CHC CHD
NA  C1A C2A C3A C4A
CMA CAA CBA
CCA
NB  C1B C2B C3B C4B
CMB CAB CBB
NC  C1C C2C C3C C4C
CMC CAC CBC CGC O1C O2C
ND  C1D C2D C3D C4D
CMD CAD CBD CGD O1D O2D
rsfit_PHE T 1 70
N CA C O CB

where the first digit gives the number of rows to read in and the second is the maximum length of the row (?).
Each record contains the atoms to include in the fit for each type of residue.