Merge_atoms

Merge_atoms [from_molecule, zone_start zone_end] [to_molecule start] [transformation matrix]

This command allows one to merge a zone of atomic coordinates in one molecule, into another molecule,with an optional transformation applied. The transformation is a database vector of 12 numbers. They can be the same molecules, and the from zone can overlap with the to zone. The command can be used to :

• Correct out of register errors, e.g.

  merge_atoms a27 a100 a110 a27 a101 ;
  

  Each residue would need updating with Lego_side_chain or Lego_auto_sc.

• If one has a number of molecules in the asymmetric unit, to paste the coordinates of one into the other e.g.

  merge_atoms a27 a100 a110 b27
  

  .lsq_rt_a_to_b where we assume a transformation .lsq_rt_a_to_b relating molecules A27 and B27.

• Generate a complete molecule from CA coordinates. If the complete molecule is called M1 (made with Sam_init_db ), and the CA's are stored as M1CA, then

  merge_atoms m1ca 1 130 m1 1 ;
  

  Then use Lego_auto_mc and Lego_auto_sc.