Macros

Some example .edp files, which can be found in the edp_data directory:

acc.edp , avb.edp , chi.edp , fix_hand.edp , find_helices.edp, find_strands.edp, matche3d.edp , phipsi.edp , set_chi.edp , set_phipsi.edp, sumw.edp and symmetry.edp .

The .edp macro file is used to save typing for a repeated calculation. The default file type of the command file is .edp (for both the VMS and the unix versions). The macros listed in this section may also be used as templates. The .edp file saved using the QUIT SAVE command may also be modified as a template macro file. The following .edp files are available in the edp_data: directory for the VMS version of EDPDB, and in the edp_data/ directory for the unix version. If one does not have a file of the identical name in the current directory, the following examples can be used directly.

acc.edp

Calculate the solvent accessible area of the given residue in the context of the rest part of the protein.

Syntax:
@acc res_id

Examples:
1) Calculate the solvent accessible area of residue 99.

      @acc 99

avb.edp

Calculate the average B of the each residue, its main chain atoms and its side chain atoms, store these values in the x, y, z fields of the CA atom.

Syntax:
@avb

Examples:
1) Make a PDB format file of the B factor information.

      @avb
      write avb.pdb

chi.edp

Calculate the chi-I, chi-Ib (if exists) and chi-II of each residue, store them in the x, y, z fields of the CA atom.

Syntax:
@chi

Examples:
1) Make a PDB format file of the chi angle information.

      @chi
      write chi.pdb

fix_hand.edp

Brucely fix all backbone chirality problems of L-amino acid residues.

Syntax:
@fix_hand

find_helices.edp, find_strands.edp

Calculate the phi, psi angles of each residue, and write a chain mark 'h' to those Ca atoms that have alpha conformation in five successive residues, or write a chain mark 's' to those Ca atoms that have beta conformation in five successive residues.

Syntax:
@find_helices
@find_strands

matche3d.edp

Overlay one protein molecule to its homologous mate based on secondary structure alignment. (It may not work for proteins which have very few secondary structures). Insertions/deletions are allowed between the two protein molecules.

Syntax:
@match3d chain_mark_1 chain_mark_2

Examples:
1) Overlay molecule B to molecule A.

      ! read in molecules A and B.
      ! match3d mainly does two things. first it calculates 
      !  the rotation-translation matrix from one molecule (B)
      !  to the other (A), named as b_to_a.dat in this
      !  example; second, it creates a PDB file, 
      !  tmp.pdb of the rotated-translated molecule (B). 
      !  the input PDB file(s) are reset to the oringinal ones
      !  at the end of the procedure.
      @match3d a b

phipsi.edp

Calculate the phi, psi angles of each residue, store them in x, y fields of the CA atom. The result can be output to a PDB format file using WRITE command.

Syntax:
@phipsi

Examples:
1) Make a PDB format file of the phipsi information.

      @phipsi
      write phipsi.pdb

set_chi.edp

This macro can be used to set the side chain torsional angles of one of the twenty natural amino acid residues.

Syntax:
@set_chi residue_id chi_1 ...

Examples:
1) Set side chain torsional angles of the residue 12 (e.g. Lys) to -60.0, 180.0, 180.0, 180.0 degrees.

      @set_chi 12 -60.0 180.0 180.0 180.0

set_phipsi.edp

This macro can be used to set the backbone torsional angles (phi and psi). It will affect the coordinates from the given residue to the end of the peptide.

Syntax:
@set_phipsi residue_id phi psi

Examples:
1) Set backbone phi-psi angles of residue 12 to -60.0, -40.0 degrees.

      @set_phipsi 12 -60.0 -40.0

sumw.edp

Calculate the summation of W value for each residue, its main chain atoms and its side chain atoms, and store them in the x, y, z fields of the CA atom.

Syntax:
@sumw

Examples:
1) Make a PDB format file of the solvent accessible area information.

      initial
      more from { ca }
      access
      @sumw
      write saa.pdb

symmetry.edp

This macro contains symmetry operators for most of the space groups that a protein crystallographer may need. It may also be used as an example file for using the GOTO/label:/RETURN statements.

Syntax:
@symmetry space_group_name

Examples:
1) To input symmetry operators for space group P212121.

      @symmetry  p212121