ono

#write the pasth + ono :

#/usr/local/src/O/ono

A) s_a_i xxx.pdb

B) mol xxx

C) z ; end

D) how insert (build):
Open xdlmapman
1. read 2fo-fc.map into  xdlmapman
2. Normalise
3. Bones skeletonise  1
4. Step size 0.5
5. Bones write to O file    bones.odb  (or other name if more than one)
                                         SKEL (or other name if more than one)
                                          5 (default)
in O:
1. read_formatted  bones.odb
2. bones-setup     
               Object name: [SKEL] skel
               Sphere raduise:  [20.0] 20.0
               What bone levels [1] : 3
3. bone-draw
4. mol
5. obj ca ca ; end
6. mutate-ins 
      mol (chose the right mol)
After which residue: a122
new residue name and type:   a123 ala
new residue name and type:   a124 ala
new residue name and type:   a125 ala
new residue name and type:   a126 ala
new residue name and type:   enter
There are 4 mutations
7. obj ca ca ; end
8. bone-ca-id
        mol
        Start at residue: a123
Backwards or Forwards (B/[F])

   Now click on the skeletone in the right order (registration)
9. Save
10. grab_atom (or move-atom) to make it better

11. lego setup
12. lego-ca  (chose the  new backbone in steps including overlaps from the nown structure and during the walk)
13. lego-auto-mc (like above)
14. obj ca ca ; end
15. (Save ; mol; zone; end ... if need)
16. lego-side-ch (for rotamers if any)
 

E) how to refi?:
1.  refi_init
2. refi_gen
3. refi_zone ...

4. To @Save_as New binary.o file:
db_kill press enter and then
FILE_O_SAVE
Then save the file with new name.

E) save as xxx.o (O 7.x: read refi_aa.o -> refi_init -> object_name -> refi_gen -> objet_name)

How to produce figures with O:

try this : http://alpha2.bmc.uu.se/~markh/notes/howto/images_howto.html

or
1. Generate a pdb file contain only the residues (substrate and/or water..) for the figure.
2. read in the file to O (s-a-i file_name -> mol file_name -> z ; end)
3. map_file filename_map
4. map_par box. box. box. sigma(0.31=1 e.g.) color sky_blue 0.5 0.1 1
5. map_cover pdb_filename (object)
_____________________________________raduis=0.75
6. map_object fig1map1
7. map_draw

CCP4 on fab / bio / eno / dam or ace:

1. in the file ccp4/ccp4.setup
should be :
setenv CCP4_SCR /usr/local/tmp/$USER # edit this if necessary

be sure that /tmp/pereg is exist
and also /usr/local/tmp/pereg is exist
type 2 times ccp4 .... befor starting work with ccp4.

surface contact:

pdb_file name= accessin
run with command:
access1
output file will be accessout (cp the results to new file named RICH.DT.
run ../bried2 output = BURIED.DAT contain surf and fractional surf.

how to tar?

to tar a dir1 to anew archive big.tar, type :

tar -cvf big.tar dir1

to un-tar a big.tar open new dir go into it new dir and, type:

tar -xvf big.tar

To compress a file :

compress bigfile

or

gzip bigfile

or to compres a tar file :

compress bigfile.tar

or

gzip bigfile.tar

to un-compress:

gunzip filenane

or

uncompress filename

to uncompress and to untar a compressed-tar file type:

gunzip < bigfile.tar.gz | tar -xvf -

or

uncompress < bigfile.tar.comprs | tar -xvf -

batch

xxx.com > xxx.log

Ctrl+D
 

Rasmol>restrict (within (5.0,*a) and *b) or (within (5.0,*b) and *a)