Q.075 - How do I create an empty poly-Ala molecule ?

Category: S.075 - build

Use the following sequence of commands:

  O > db_create
 Heap> Name of new data block: new_residue_type
 Heap> How many elements in data block: 131
 Heap> Type of elements (T,C,[I],R): c
  O > db_set_dat
 Heap> Full name of data block: new_residue_type
 Heap> It is of type C and has 131 entries
 Heap> Start and end entries [1 131 ]:
 Heap> Changing entries 1 to 131 of data block new_residue_type
 Heap> Enter value (must be type C): ALA
  O > write new_residue_type ;;
 NEW_RESIDUE_TYPE          C        131 (1x,5a)
 ALA   ALA   ALA   ALA   ALA
 ALA   ALA   ALA   ALA   ALA
 ...
 ALA   ALA   ALA   ALA   ALA
 ALA
  O > sam_init
 Sam> This WILL initialise certain datablocks.
 Sam> Molecule name ([] to exit): new
 Sam>  Database compressed.
 Sam> Making residue names.
 Sam>  There are   131 residues,  655 atoms.
  O > dir new_*
 Heap>  NEW_RESIDUE_TYPE          C W       131
 Heap>  NEW_RESIDUE_NAME          C W       131
 Heap>  NEW_ATOM_NAME             C W       655
 Heap>  NEW_ATOM_XYZ              R W      1965
 Heap>  NEW_ATOM_B                R W       655
 Heap>  NEW_ATOM_WT               R W       655
 Heap>  NEW_ATOM_Z                I W       655
 Heap>  NEW_ATOM_SELECT           I W       655
 Heap>  NEW_ATOM_VISIBLE          I W       655
 Heap>  NEW_RESIDUE_POINTERS      I W       262
 Heap>  NEW_RESIDUE_CG            R W       524

You'll need this when you have finished tracing and touching up the skeleton and are about to start using the Baton or Bone_Pick_Ca commands to put in alpha carbon atoms.