bones

Convert an electron density file into a skeleton with an O data structure. This is a formatted data structure so if the calculation is run on a VAX, it can be ftp'ed and read into your Unix machine when starting O or with the Read_formatted command.

In the example, we define a start level approximately 1.3 sigma, and a step of sigma. It is also necessary to decide what skeleton atoms are to be classified as main chain and side chain. This is done by defining a minimum connection length of 8. The user also specifies the molecule name to be associated with the skeleton. The resulting file is formatted. The following output has been edited to remove CCP4 excess listings.

 
% ../bin/bones 
 electron density file name:  ano1.E 
 map type ([ccp4]) :  ccp4 
 base level and step level for skeletonising :  .020 .015 
 Fourier parameters as read from the data-set
          Origin ................................    0    0    0
          Extent ................................   76   84   48
          Grid ..................................   76   84   48
          uvw (fast, medium, slow) ..............    Z    X    Y

          base level .......................................   0.020
          level increment ..................................   0.015
          number of levels .................................       5

 input map contains 24242 points (level>0)
 skeletonized map contains  7698 points (level>0)
no. of points in the bones : 7798( including spare points)
                     no. of spare points        :     100
                     no. of connections         :    8349
                     no. of branch-points       :    1058
                     no. of fragments
                                    size .le.  1 :  372
                                    size .le.  5 :  790
                                    size .le. 10 :   24
                                    size .le. 50 :   56
                                    size .le.100 :    6
                                    size .gt.100 :    4

 Length to define skeleton as main chain : 8 
                     minimum mainchain lenght     :       8
                     no. of mainchain connections :    3875
                     no. of sidechain connections :    4473
 O Bones file name : q_skl.o 
  Histogram of bones types 1,2,3....
  Bone Type:     1  3893  3804   100     0     0     0     0     0  
 Associated O name: ano1 
vega [36]#  grep ANO1 q_skl.o
ANO1_ATOM_XYZ             R     23394 (3f10.3)
ANO1_ATOM_BONE            I      7798 (5i10)
ANO1_CONNECTIVITY         I      8349 (5i10)
ANO1_ATOM_COLOUR          I      7798 (5i10)
ANO1_RESIDUE_NAME         C         1 (5a)
ANO1_RESIDUE_TYPE         C         1 (5a)
ANO1_RESIDUE_POINTERS     I         2 (5i10)
vega [37]#