O


PEPFLIP

This commands calculates the orientation of the peptide oxygens atoms
and compares it to the database.
Values higher than 2-2.5 should be checked !

- Syntax :
pep_flip a 1 100 (do pep_flip on molecule a from residue 1 to 100)

- Output :
Util> Calculating zone 1 to 100 in molecule A , object AALL
Util> The DB is now being loaded.
Util> Loading data for protein: HCAC
.....
Util> 20 fragments used for residue 3 pep_flip value= 1.41
Util> 20 fragments used for residue 4 pep_flip value= 1.32

RSR

In order to find the correlation between the electron density map and the model, type:

rsr_map
RSR> Name of map file? [../../../refinement/stage01/amore/3fo2fc_map.dn6]:
read odat/rsfit_all.o
rs_fit A06 A21 A258

NB: 'odat' is the link for /whatever/o/data/.
In this directory there are different files which allow to calculate the map-to-model correlation
1) for all the residues (main and side chain) - /whatever/o/data/rsfit_all.o
2) for the main chains only -/whatever/o/data/rsfit_mc.o
3) for the side chains only - /whatever/o/data/rsfit_sc.o

NB: rs_fit A06 A21 A258, in this example
1) 'A06' is the molecule name
2) 'A21' is the first residue in molecule A06
3) 'A258' is the last name in molecule A06

'O' will then list all the correlations like:

Util> Plus value for this map is: 80
Util> 9 atoms for residue A251 correlation= 0.551
Util> 9 atoms for residue A252 correlation= 0.736
Util> 7 atoms for residue A253 correlation= 0.678
Util> 9 atoms for residue A254 correlation= 0.678
Util> 9 atoms for residue A255 correlation= 0.468
Util> 26 atoms in zone
** BEST CORRELATION = 1.0
** WORST CORRELATION = 0.0

take the all correlation list and paste it into a file sort this file in ascendent order of correlation:

grep correl a.a | sort +7 > b.b

(sort -r +7 allows to sort in REVERSE order!!!!!)

Now I can use the file b.b as a guide to understand the worst correlation,
hence the residues that I have to check in the map.

RSC_FIT

This command calculates the rmsd with the rotamer that is most similar 
to your sidechain conformation. Values greater than 1.5 A (or 1 A for leu and ile) 
should be checked!

- Syntax:
rsc_fit a 1 100 (do rsc_fit on molecule a from residue 1 to 100)

- Output:
Util> A 1 100 AALL
Util> The ~Rotamer_DB is now being loaded.
Util> Calculating zone 1 to 100 in molecule A , object AALL
Util> All atoms in this residue are fixed
Util> SCGLY is missing.
Util> Best rotamer for 4 is No. 1 with rms 0.159
Util> Best rotamer for 5 is No. 1 with rms 0.855
Util> Best rotamer for 6 is No. 1 with rms 0.223
.....

RS_FIT

This commands calculates how well your model fits the 2Fo-Fc map.
First, one has to change the settings.
O >map_file
Map> Name of map file? [fofc.o]: 2fofc.o
O >rsr_map
RSR> Name of map file? [2fofc.o]: 2fofc.o
O >rsr_setup
RSR> Automatic scaling? [No]: yes
RSR> autoscale option on
RSR> Contouring of refinement box? [No]:
RSR> Which metod, CONV or DIFF? [CONV]:
RSR> Maximize the convolution product
RSR> Real space R factor(RFAC) or Correlation coefficient(RSCC)? [RSCC]: rfac
RSR> Attempt to subtract out neighbour atom density? [No]:
RSR> Define number of scans [5]: 5
RSR> Define shifts [ 0.30 0.20 0.10 0.10 0.05]:
RSR> Define overall B [ 20.00]:
RSR> Define wall [ 3.50]:
RSR> Define C and Ao [ 1.04 0.90 ]: 0.95 0.90
RSR> Define integration radius [ 3]:
RSR> Define scale to be applied to calculated density [ 50]:

- Syntax:
rs_fit a 1 100 (do rs_fit on molecule a from residue 1 to 100)

- Output:
Util> A 1 100 AALL
Util> Calculating zone 1 to 100 in molecule A , object AALL
Util> 32 atoms in zone
Util> Plus value for this map is: 62
Util> 5 atoms for residue 1 R factor= 0.331
Util> 4 atoms for residue 2 R factor= 0.331
Util> 7 atoms for residue 3 R factor= 0.201
Util> 5 atoms for residue 4 R factor= 0.181
Util> 11 atoms for residue 5 R factor= 0.253

Paint command

Affects the colour properties of molecules or molecular objects. Each molecule has an associated atomic property called <mol>_atom_colour, and each molecular object has a property called .obj_col_<object_name>.

The normal way to specify colours in O is by typing the name of a color. In the default startup.o and colour_default.o files, there are 71 colors to choose from and are the colors defined in X-windows.

These are:

O > paint_col ?
Paint>Available colors:
Paint> aquamarine black blue
Paint> blue_violet brown cadet_blue
Paint> coral cornflower_blue cyan
Paint> dark_green dark_olive_green dark_orchid
Paint> dark_slate_blue dark_slate_gray dark_slate_grey
Paint> dark_turquoise dim_gray dim_grey
Paint> firebrick forest_green gold
Paint> goldenrod gray green
Paint> green_yellow grey indian_red
Paint> khaki light_blue light_gray
Paint> light_grey light_steel_blue lime_green
Paint> magenta maroon medium_aquamarine
Paint> medium_blue medium_forest_green medium_goldenrod
Paint> medium_orchid medium_sea_green medium_slate_blue
Paint> medium_spring_green medium_turquoise medium_violet_red
Paint> midnight_blue navy navy_blue
Paint> orange orange_red orchid
Paint> pale_green pink plum
Paint> red salmon sea_green
Paint> sienna sky_blue slate_blue
Paint> spring_green steel_blue tan
Paint> thistle turquoise violet
Paint> violet_red wheat white
Paint> yellow yellow_green

If this is not enough for you, the program will in most places accept 3 numbers for the RGB value when the colour prompt comes up. To get the list of colour names, type a question mark (?) as argument to the Paint_colour command. When specifying a colour name, you are allowed to abbreviate to a unique set of letters.

Symm_setup

In order to create symmetry related molecules:

mol cns01
symm_set
symm_cell
symm_obj [INPUT OBJECT NAME AND NOT MOL NAME, IE ~CNS01C]

In order to be able to click on a residue belonging to a symmetry related molecule, instead of doing

symm_set
symm_obj

use:

symm_set
symm_sphere

It will produce different symmetry related molecules that can be clicked.

Symm_setup
[space group 96---P43212, 92---P41212]
Symm_cell

Convert CCP4 or CNS maps to .dn6

6d_mapman
MAPMAN > read
New map ? ( ) m1
File name ? (not_defined) resolve.ext
Format ? (~CCP4) (or CNS if CNS maps)

Often in mapman you may get the following error:

ERROR  Map too big !
Requested size : ( 4465674)
Available size : ( 4194304)
ERROR  Sorry !
ERROR  While opening map file

In this case type '?'

MAPMAN > ?

It gives a list of options; in this case use

MAPMAN > ~ZP_restart mapsize
ERROR  While reading integer from input string
MAPMAN > ~ZP_restart
New MAPSIZE ? ( 4194304) 4465674
New NUMMAPS ? ( 2)

Allocate maps of size : ( 4465674)
Max number of maps : ( 2)

and then read map again:

MAPMAN > normalize
Which map ? (m1)
MAPMAN > mappage
Which map ? (M1)
Brick file ? (resolve.map) resolve.dn6
MAPMAN > quit
WARNING - unsaved changes to map M1 !!!
Do you really want to quit (Y/N) ? (N) Y

CIS Proline

In order for O to understand that it is CIS and allow to do regularize on it without making it back as TRANS, you need to edit the pdb file and change PRO to CPR (now O will understand CIS-PRO). 

LSQ

HOW TO ROTATE MOLECULE AB15 ON MOLECULE B01:

lsq_exp
Lsq > Least squares match by explicit definition of atoms.
Lsq > Given 2 molecules A, B the transformation rotates B onto A
Lsq > What is the name of A (the not rotated molecule)? B01
Lsq > What is the name of B (the rotated molecule)? ~AB15
Lsq > Now define what atoms in A [=B01] are to be matched to B [=~AB15]
Lsq > Defining 3 names in B01 implies a zone and an atom name.
Lsq > Defining 2 names in B01 implies a zone and CA atoms.
Lsq > Defining 1 name in B01 implies the CA of that residue.
Lsq > Molecule ~AB15 just requires the start residue and atom name.
Lsq > A blank line terminates input.
Lsq > Define atoms from B01 (the not rotated molecule): B122 B258
Lsq > Define atoms from ~AB15 (the rotated molecule): A122
Lsq > Define atoms from B01 (the not rotated molecule):
Lsq > The 137 atoms have an r.m.s. fit of 0.230
Lsq > xyz(1) = 0.7179*x+ 0.6958*y+ 0.0232*z+ -45.1274
Lsq > xyz(2) = 0.6959*x+ -0.7181*y+ 0.0062*z+ 105.7454
Lsq > xyz(3) = 0.0210*x+ 0.0117*y+ -0.9997*z+ 192.3656
Lsq > The transformation can be stored in O.
Lsq > A blank is taken to mean do not store anything
Lsq > The transformation will be stored in .LSQ_RT_junk1

lsq_mol
Lsq > Apply a transformation to an existing molecule.
Lsq > There are these transformations in the database
Lsq > JUNK ~JUNK1
Lsq > Which alignment [<CR>=abort operation] ? ~JUNK1
Lsq > There these molecules in the database
Lsq > ALPHA BETA DI MUT CC
Lsq > WAT MIN B01 ADP P1 P2
Lsq > BASE ~ADP1 DC A08 ~SYM1 ~SYM2
Lsq > PEAK SCCYH SCALA SCLEU SCPRO SCTHR
Lsq > SCCYS SCHIS SCILE SCMET SCSER SCVAL
Lsq > SCPHE SCARG SCTYR SCTRP SCASP SCASN
Lsq > SCGLU SCGLN SCLYS A15 ~AB15
Lsq > Which molecule? [<CR>=abort operation]: ~AB15
Lsq > Define a zone in which to apply the tranformation [all]:
mol ~AB15
obj
Mol> Name of the new object [~AB15 ]: ~AB15c
ca ; end
obj
Mol> Name of the new object [~AB15 ]: ~AB15z
z ; end

PDBSET

PDBSET Matrix from lsq_expl
copy the matrix after lsq_expl or better lsq_impr digit in a shell:

pdbset xyzin 1.pdb xyzout 2.pdb

where 1.pdb is the pdb I want rotate on 2.pdb. Then when pdb stop insert the matrix in this format:

TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz

or:

TRANSFORM [INVERT] ODB [O_database_filename]

Mutate 

- mutate_replace
mut_repl

it will ask for chain, number residue, and residue kind in which to mutate

- mutate_insert
edit text pdb file and duplicate aminoacid preceeding the position in which to insert the new one, then modify of 1 X, Y or Z save and read again in O the pdb. From O then modify the position of the new inserted residue with move_fragment or move_zone.

- mutate_delete
edit test pdb file and remove the residue we want to delete, save and read again into O.

Torsion files

1. prepare pdb file
2. run 6d_moleman
3. use option "TORSion_datablock"
4. this will output a *.dat file. This is the file that O needs.
5. copy torsion.o (from the odat directory) to my directory (why? - so that I could edit and change the file).
6. edit torsion.o; append the file output by 6d_moleman to torsion.o

[Make sure to change the number of lines in the file- this number is written in the first line of the file torsion.o]

7. read file torsion.o into O: use the command: read torsion.o
8. Go to O graphics window, chose tor_residue from the Rebuild menu, and click on any atom of molecule.