How To ....

Start EDPDB, get help and Quit
Calculate ...
Edit a PDB file
Apply the crystallographic symmetry
Others

Start EDPDB

This paragraph discusses how to start EDPDB from a (VMS) DCL command line.

Syntax:
$ EDPDB [file_name_1 [mark_1]] [file_name_2 [mark_2]] [/EDPINI[=edp_file]]

Note:
1) A mark is a character string which can be used to distinguish different peptide chains. It is particularly useful when more than one PDB files are read in and the peptide chains need to be distinguished. Whenever a new chain is found, its chain name will be replaced with a new character in the character string of the mark, unless the character is an underscore `_'. In the latter case (which is the default), no substitution will be made. If all of the characters in the string have already been used, it starts from the first character of the string again. A string of mark characters of alphabetic order may be abbreviated with a hyphen, `-'. For example, a-f is equivalent to abcdef.
2) For the VMS version, the default file type of the input file is .pdb.
3) The edp_file is the file name of a macro which can be used to customize the initial configuration of EDPDB. The default file name is edpini.edp, if the qualifier /EDPINI is specified.

A quick check

      ! Try this
      initial
      zone all
      zone 
      residue
      atom
      sort dfres
      analyze

Input multiple PDB files

1) Read in two files which have the same chain names (eg. A,B,C and D)

      read  file_a.pdb  abcd  initialize
              ; input the first file, keeping the chain names
      read  file_b.pdb  efgh
              ; input the first file, change the chain names
              ; to E,F,G and H

2) or start the program by typing

      $ edpdb file_a.pdb abcd file_b.pdb efgh

Save the intermediate result

1) If the result can be listed with the LIST command, WRITE command can be used to make an output file to save the result.

2) If the result is listed on the terminal with a prompt saying " return for more ... ", the result actually has a copy in a file of the same file-name as the 1st input PDB file and a file type of .scr. To save this file, one has to terminate the program using the QUIT command with the SAVE option.

3) To save other intermediate results, one may either run EDPDB in a batch job mode, or redirect the result to a file (eg. edpdb.log) using the following command.

      file log edpdb.log

List the currently opened files

      file

List the header of the 1st input PDB file

      initial
      write junk.pdb header

Restart without quitting

      reset

Coordinate transformation

1) Command mode. Assume the transformation matrix has been stored in a file rtn.dat

      ! select the records on which the transformation are applied.
      ...
      rtn file rtn.dat

Superimpose two structures

Overlay molecule A to molecule B, based on the least square minimization between main-chain atoms of the two molecules.

      group mola from { main from { chain a }}
      group molb from { main from { chain b }}
      initial
      load mola
      overlay molb rtn.dat
      chain a
      rtn file rtn.dat

Matrix manipulation

1) Copy the transformation matrix in the file rtn_a.dat to a file rtn_b.dat.

      initial
      rtn file rtn_a.dat save rtn_b.dat

2) Calculate the inverse transformation of a given one, eg. in file rtn.dat, store it in another file, say inv_rtn.dat.

      initial
      rtn file rtn.dat inve inv_rtn.dat

3) Multiply the transformation matrix in the file rtn.dat with the matrix of symmetry operator #2, store the production in rtn.dat.

      initial
      rtn symm 2 0 0 0 mult rtn.dat rtn.dat

Calculate solvent accessible area

An isolate protein molecule (eg. zone 1 - 164).

      initial
      zone 1 - 164
      access

Calculate buried solvent accessible area

1) The buried solvent accessible area (SAA) of molecule A by molecule B equals the difference between the SAA of molecule A in the presence and absence of the molecule B. Note that the buried SAA of molecule A by molecule B is not necessary to equal the buried SAA of molecule B by molecule A.

      initial
      group molB from { chain B}
      chain A
      access molB
           ; get the SAA of molecule A
           ; in the presence of molecule B
      access
           ; get the SAA of molecule A
           ; in the absence of molecule B

Calculate distance

1) List distance pairs between two groups of atoms. For example, the distances between oxygen atoms and nitrogen atoms.

      group Natm from { atom N* }
      group Oatm from { atom O* }
      initial
      load Oatm
      distance Natm 0.0 3.5 2 2000

Calculate angle

1) List all the C-alpha - C-beta - C-gamma angles.

	dfabc ca cb cg 0 0 0
	initial
	atom ca cb cg
	abc

2) Calculate the angle that formed by atoms from different residues, eg. the C-O-OH angle, where C and O are the carbonyl carbon and the carbonyl oxygen atoms of an amino acid residue and OH is a water molecule.

	dfbrg C O OH CA x 0 x 0  ,,,,  0.0 3.5 0.0 180.0 0.0 360.0 zwxy
		; The 1st 'x 0' indicates that the C atom (atom_w) belongs
		; to the same residue as the O atom (atom_x).
		; The 2nd 'x 0' indicates that the CA atom (atom_z) also 
		; belongs to the same residue as the O atom (atom_x).
		; The O-OH distance, the C-O-OH angle and CA-C-O-OH torsion
		; angle will be calculated.
	initialize
	atom C O OH
	bridge

Calculate torsional angles

1) Calculate the phipsi torsional angles

      @phipsi
      write phipsi.lis

2) Calculate the chi (I,II) angles.

      @chi
      write chi.lis

3) Calculate the zeta angles to check chirality.

      initial
      dfabcd ca n c cb
      atom ca n c cb
      abcd
      quit save

See also: ABCD command and RTN ABCD command.

Disulfide bridge geometry and prediction

1) Define a bridge of disulfide bond, and list out all the bridges.

      dfbrg cb sg sg cb x 0 y 0
      residue cys

2) Search for candidates of sites of engineered disulfide bridges. The search criterion is the following. The two residues should be 20 residues apart in the amino acid sequence. The Cb-Cb distance should be between 2.5 and 6.0 Å. One of the Ca-Cb-Cb angle should be between 80.0 and 180.0 degrees. (The Ca-Cb-Cb-Ca torsional angle is unrestricted).

      initial
      dfbrg ca cb cb ca x 0 y 0 t t t t 2.5 6.0 80 180 0 360 wxyz 20
      atom ca cb
      bridge

Hinge bending angle

Analyze the hinge bending angle between two molecules A and B, assuming that they have rigid body domains (residues 15 - 60) and (residues 80 - 160).

      initial
      group n_a from { main a15 - a60 }
      group n_b from { main b15 - b60 }
      load  n_a
      overlay n_b match_n_domain.dat
      initial
      group c_a from { main a80 - a160 }
      group c_b from { main b80 - b160 }
      load c_a
      rtn file match_n_domain.dat
      overlay c_b match_c_domain.dat
      initial
      axis match_c_domain.dat
           ; the hinge bending angle will be listed
           ; with the AXIS command.

Edit the PDB records

1) Reset the entry number

      sete

2) Split the chain name from the residue number in the input residue id.

      seti

Standardize the PDB file

See also: SORT DFRES, SETI, SETC and PERMUTE

Sort the PDB file

1) Sort the records according to B factors

      zone all
      sort B
      list

2) Sort the records according to X coordinates

      zone all
      setw x
      sort w
      list

Crystallographic symmetry

1) Input symmetry operators of space group P3(2)21 for T4 lysozyme enzyme.

      initial
      cell 61.2 61.2 96.8 90 90 120 1
      symmetry x, +y, +z
      symmetry -y, x-y, +z+2/3
      symmetry -x+y, -x, +z+1/3
      symmetry +y, x, -z
      symmetry -x, -x+y, -z+2/3
      symmetry x-y, -y, -z+1/3

2) Check the crystal packing contacts between molecules A and B.

      group mola from { chain A }
      group molb from { chain B }
      initial
      load mola
      mmig mola 4.0     ; check A-A contacts
      mmig molb 4.0     ; check A-B contacts
      initial
      load molb
      mmig molb 4.0     ; check B-B contacts

3) The solution of a molecular replacement search may put the protein molecule in an asymmetric unit which is far away from the origin. The MOVECENTER command can bring the molecule close to the origin (or any user specified asymmetric unit).

     zone all
     movecenter rtn.dat  0.0 0.0 0.0 0.5 0.5 0.5
     rtn file rtn.dat

Study a rotation function result

1) Assume that the space group is P3(2)21; the positions of the cross rotation function solution peaks are stored in a PDB format file.

	! First, input the polar angles using a PDB format file
	cell 61.2 61.2 96.8 90.0 90.0 120.0 1
		; input the cell parameters 
	@p3221
		; input the symmetry operators using a macro file
	zone all
	list	; take a look of the initial peaks
	polar to_polar 
		; standardize the angles
	list	; take a look again
	polar asymm 
		; convert the peaks to one asymmetric unit
	list	
	polar unique 3.
		; exclude redandent peaks
	list
	reset
	zone all
	polar move_to_o 1 ca
		; apply a rotation such that the first peak,
		; which is stored in the "CA" record of the residue "1",
		; will move to the origin.
	list

2) Assume that the space group is P3(2)21; the positions of the self rotation function solution peaks are stored in a PDB format file.

	! First, input the polar angles using a PDB format file
	cell 61.2 61.2 96.8 90.0 90.0 120.0 1
		; input the cell parameters 
	@p3221
		; input the symmetry operators using a macro file
	zone all
	list	; take a look of the initial peaks
	polar srf_red
		; convert the peaks to one asymmetric unit
	list	
	polar unique 3.
		; exclude redandent peaks
	list

Model mutation

1) Mutate residue at position 6 to Ile.

      initial
      zone all
      write backup.pdb   ; save the current file for safety
      @mut 6 ile         ; a VMS version
           ; to run this macro, one may need to copy the aalib.pdb
           ; to his/her current directory.

2) Set the chi-I and chi-II angles of residue 6 Ile to -60 and 170 degrees using a macro file, set_chi_ile.edp.

      @set_chi_ile  6  -60 170

where set_chi_ile.edp contains the following.

      ! set_chi_ile.edp
      initial
      side    $(p1)
      rtn abcd $(p1) n  $(p1) ca $(p1) cb  $(p1) cg1 $(p2)
      exclude atom cg2
      rtn abcd $(p1) ca $(p1) cb $(p1) cg1 $(p1) cd1 $(p3)

Fix the chirality problem

To fix a chirality problem brucely, a mirror operation has to be applied to some atoms.

1) Change the Ca position of residue 164.

      initial
      ca 164
      rtn overlay 164 N C CB 0 0 0 , ,,, ,,, inve tmp.dat
      rtn matrix  -1 0 0 0 1 0 0 0 1 0 0 0
      rtn file tmp.dat

2) Change the position of the side chain of residue 164.

      initial
      side 164
      rtn overlay 164 N CA C 0 0 0 , ,,, ,,, inve tmp.dat
      rtn matrix -1 0 0 0 1 0 0 0 1 0 0 0
      rtn file tmp.dat

Build a molecule, eg. a substrate

1) To build a molecule from scratch, See also: the examples in the NEWXYZ section

2) To build a molecule from pieces of fragments, see RTN OVERLAY command.

Analyze polar/eulerian angles

Convert polar angles to eulerian ones, assuming the x,y,z fields store the polar angles.

      zone all
      polar  to_euler