Definition

Available commands: ALIAS , CELL , DFAB , DFABC , DFABCD , DFBRG , DFCA , DFNEWXYZ , DFMAIN , DFRES and SYMMETRY .

One philosophy of EDPDB is that the user should be allowed to teach the program what to do, and EDPDB provides the algorithms about "how to do it". For example, the command DFABCD can be used to define a calculation of backbone or side chain torsion angles or any types of pseudo torsion angles, eg. a torsion angles formed with four sequential Ca atoms. As a general purpose program, EDPDB allows the user to overwrite the default definitions of the program, which might be too specific in some cases. For example, a user may use the command DFMAIN N CA C O CB to overwrite the default definition of DFMAIN N CA C O.

ALIAS

Create a User-Defined command leading Keyword (UDK in short). A UDK has higher priority than the build-in command leading keywords.

Function: Definition, Information

Syntax:
1) ALIAS
2) ALIAS xxxx
3) ALIAS xxxx yyyy
or ALIAS xxxx := yyyy
4) ALIAS xxxx ''
or ALIAS xxxx :=

Note:
1) The xxxx stands for a UDK which is a character-string of up to 8 characters; and the yyyy stands for a text-string of up to 60 characters, which will replace the UDK during command interpretation.
2) The first form lists the current available UDKs. The second form shows the current definition of the UDK specified. The third form defines a new UDK, or overwrites the old one (if one exists) with the new definition. And the fourth form deletes the specified UDK by assigning an empty string to it.
3) Up to ten keywords can be defined simultaneously. Over ten definitions will overwrite the earlier defined alias permutatively.
4) To prevent a looped definition, during command interpretation, each UDK substitution increases the number of accumulated errors by one. Error message will be given if the number of error exceeds max_err, (see MAXERR command).
5) Since a UDK has higher priority, it may prohibit the function of some built-in commands. For example, a user-defined keyword cake will deactivate built-in EDPDB commands C and CA until the definition of cake is deleted. One way to avoid this problem is to add a prefix, eg. an underscore `_' or a dollar sign $, to the UDK.

See also: PARAMETER and maximum number of user-defined keywords

Examples:
1) An example macro to define keywords for calling some VMS commands. 

      ! vms.edp
      alias dire      system wait dire
      alias type      system wait type/page
      alias edit      system wait edit/edt
      alias show      system wait show
      alias copy      system wait copy
  or
      ! vms.edp
      dire :=         system wait dire
      type :=         system wait type
      edit :=         system wait edit
      show :=         system wait show
      copy :=         system wait copy
2) List the PDB files in the current directory. 
      alias dire system wait directory
      dire *.pdb

CELL

Define the cell parameters and the convention used to align the (xyz) Cartesian coordinate systems relative to the crystallographic axes, a, b and c.

Function: Definition, Information

Syntax:
1) CELL
2) CELL [a b c alpha beta gamma] [convention#]

Note:
1) The first form displays the current cell parameter information.
2) The second form defines the cell parameters. It also initializes the current symmetry information. The default value is the corresponding old value, if it exists.
3) If no cell parameters have been defined when they are required by the program, the cell parameters from the 1st input PDB file will be used, if they exist.

See also: RTN, SHDF and SYMMETRY

Convention#
The convention number is an integer between 1 and 8.

1: x//a*, y//b, z//(a* X b)
2: x//(b X c*), y//b, z//c*
3: x//(b* X c), y//b*, z//c
4: x//a*, y//(c X a*), z//c
5: x//a, y//(c* X a), z//c*
6: x//a, y//b*, z//(a X b*) -- #6 is the convention used by FRODO
7: x//(a-b), y//(a+b-2c), z//(a+b+c) -- only for R+ lattice
8: x//(a-c), y//(2b-a-c), z//(a+b+c) -- only for R- lattice

Examples:
1) Display the current cell parameters and the alignment convention. 

      cell
2) To define the cell parameters (eg. of T4 lysozyme P3(2)21 crystal form) and the alignment convention x//a*, y//b, z//(a* X b). 
      cell 61.2 61.2 96.8 90.0 90.0 120.0 1

DFAB

Define a template for distance pair search.

Function: Definition, Information

Syntax:
1) DFAB
2) DFAB atom_a atom_b [reg_a reg_b] [status_a status_b] [Dmin Dmax]

Note:
1) The first form shows the current AB definition.
2) The atom_x is the atom name (eg. Ca, OG).
3) The reg_x is the relative registration number, which is an integer. The default is 0.
4) The status_x is either a T (stands for true) or an F (stands for false). It determines whether the calculation is based on an ON atom for the corresponding position or not. The default is T, which means an ON atom is required for the calculation.
5) Only will the distance smaller than the Dmax and larger than the Dmin be listed. The default Dmin and Dmax are 0.0 and 99.0.

See also: AB, DFABC, DFABCD, DISTANCE and SHDF

Examples:
1) Define every N, CA atoms in the same residue as a distance pair. 

      dfab n ca
2) Define the Ca atomS in the (i)th and (i+1)th residues as a distance pair. 
      dfab ca ca 0 1
3) Calculate the distance from the O atom in the (i)th residue to the N atom in the (i+4)th residue, and list the result if the O atom is selected as an ON atom and the distance is between 2.0 and 3.5 A. 
      dfab o n 0 4 t f 2.0 3.5
      atom o n
      ab

DFABC

Define a template for an angle group search.

Function: Definition, Information

Syntax:
1) DFABC
2) DFABC atom_a atom_b atom_c [reg_a reg_b reg_c] [status_a status_b status_c] [Amin Amax]

Note:
1) The first form shows the current ABC definition.
2) The atom_x is the atom name (eg. Ca, OG).
3) The reg_x is the relative registration number, which is an integer. The default is 0.
4) The status_x is either a T (stands for true) or an F (stands for false). It determines whether the calculation is based on an ON atom for the corresponding position or not. The default is T, which means an ON atom is required for the calculation.
5) Only will the angle smaller than the Amax and larger than the Amin be selected. The default Amin and Amax are 0.0 and 180.0 degrees.

See also: ABC, DFAB, DFABCD and SHDF

Examples:
1) Define every N, CA and CB atoms in the same residue as an angle group. 

      dfabc n ca cb 0 0 0 t t t 0.0 180.0
2) Define the CA atoms in the (i-1)th, (i)th and (i+1) residues as an angle group. 
      dfabc ca ca ca -1 0 1
3) Calculate the angles formed with Ca-C-O atoms in the same residue and larger than 135.0 degrees 
      dfabc Ca C O  ,,,  ,,,  135.0 180.
      atom Ca C O
      abc

DFABCD

Define a template for a torsion_anglesearch.

Function: Definition, Information

Syntax:
1) DFABCD
2) DFABCD atom_a atom_b atom_c atom_d [reg_a reg_b reg_c reg_d] [status_a status_b status_c status_d] [Tmin Tmax]

Note:
1) The first form shows the current ABCD definition.
2) The atom_x is the atom name (eg. Ca, OG).
3) The reg_x is the relative registration number, which is an integer. The default is 0.
4) The status_x is either a T (stands for true) or an F (stands for false). It determines whether the calculation is based on an ON atom for the corresponding position or not. The default is T, which means an ON atom is required for the calculation.
5) Only the angles that are smaller than the Tmax and larger than the Amin will be selected. The default Tmin and Amax are - 180.0 and 180.0 degrees.

See also: ABCD, DFAB, DFABC, RTN and SHDF

Examples:
1) Define every N, CA, CB and CG atoms in the same residue as a torsion_anglegroup (ie. chi-I) which ranges between 0.0 and 360.0 degrees. 

      dfabcd n ca cb cg 0 0 0 0 t t t t 0.0 360.0
2) Define the CA atoms in the (i)th, (i+1)th, (i+2)th and (i+3)th residues as a torsion_anglegroup. 
      dfabcd ca ca ca ca 0 1 2 3
3) Calculate the peptide phi torsion angles which range between (- 90.0) and 0.0 degrees. 
      dfabcd  c n ca c 0 1 1 1  ,,,,  -90.0 0.0
      atom c n ca c
      abcd

DFBRG

Define a template for a BRIDGE group search.

Function: Definition, Information

Syntax:
DFBRG atom_w atom_x atom_y atom_z [Rw reg_w Rz reg_z] [status_w status_x status_y status_z] [Dmin Dmax Amin Amax Tmin Tmax] [(WXYZ, ZWXY)] [skip]

Note:
1) The atom_w etc. are atom names (eg. Ca, OG).
2) Rw and Rz are either X or Y, indicating whether the atom_w or atom_z is registered relative to atom_x or atom_y. The default is X.
3) The reg_w and reg_z are (integer) registration numbers of atom_w and atom_z. The default is 0.
4) The status_w etc. are either T (stands for true) or F (stands for false). It determines whether the calculation is based on an ON atom for the corresponding position or not. The default is T, which means an ON atom at that position is required for the calculation.
5) Dmin, Dmax, Amin, Amax, Tmin, Tmax are the selection criteria of the X-Y distance, the W-X-Y angle and the W-X-Y-Z or Z-W-X-Y torsion angle. The default values are 1.0, 4.0 Å, 90.0, 120.0 degrees, and 0.0, 360.0 degrees respectively.
6) The torsion angle is defined as W-X-Y-Z if WXYZ option is used or by default; it can also be defined as Z-W-X-Y using the ZWXY option.
7) The integer skip is the minimum atom_x - atom_y distance in terms of the residue number in the input PDB file. The default is zero.

See also: BRIDGE, DFAB, DFABC and DFABCD

Examples:
1) Define a bridge of disulfide bond, and list out all the bridges. By default, it will looking for interatomic distance (X-Y) between 1.0 and 4.0 Å. 

      dfbrg cb sg sg cb x 0 y 0 
      residue cys
      bridge
3) Define a bridge of hydrogen bond formed between N and O atoms in the zone 1 - 60. 
      dfbrg c n o ca x -1 x 0  ,,,,  2.3  3.5  100.0  140.0 150.0 210.0 
           ; The 'x -1' indicates that the C atom (atom_w) belongs
           ; to the previous residue of the N atom. 
           ; The 'x 0' indicates that the CA atom (atom_z) belongs
           ; to the residue of the N atom.
      main 1 - 60
      bridge
           ; list all the hydrogen bonds, which have N-O bond 
           ; length between 2.3 and 3.5 Å, C(-1)-N-O angle 
           ; between 120.0(+/-)20.0 degrees, and 
           ; C(-1)-N-O-Ca torsion angle (default option WXYZ) 
           ; between 180.0(+/-)30.0 degrees.

DFCA

Redefine CA atom type.

Function: Definition, Information

Syntax:
1) DFCA
2) DFCA atom_name

Note:
The first form display the current Ca definition.

See also: AVB, CA, DFMAIN, RMSW, SHDF and SUMW

Examples:
1) Define the O5' atom as CA for a DNA molecule. 

      dfca O5'
2) Define the N atom as CA, and store the result of the AVB command to the x field of the N atom records. 
      dfca n
      avb x

DFNEWXYZ

Define the rule to create the coordinates of new points.

Function: Definition, Information

Syntax:
1) DFNEWXYZ
2) DFNEWXYZ atom_a atom_b atom_c [reg_a reg_b reg_c] [status_a status_b status_c] [distance] [angle] [torsion_angle]

Note:
1) The first form shows the current definition.
2) The atom_x is the reference atom name; the reg_x is the relative registration number (eg. the default value 0 0 0 indicates that the three atoms are in the same residue); the status_x indicates whether the reference atom needs to be selected as an ON atom in order to perform the calculation. The default is t t t (t stands for logical true).
3) The distance is the distance between the new_atom and atom_a; the angle is defined as new_atom - atom_a - atom_b; and torsion_angleis defined as new_atom - atom_a - atom_b - atom_c. The default distance, angle and torsion_angle are zeros.

See also: NEWXYZ

Examples:
1) Define the rule of creating a Tyr from a Phe, ie. the rule of create the OH atom in the Tyr. 

           dfnewxyz Cz Ce1 Cd1 0 0 0 t t t 1.38 120.0 180.0
2) Define the coordinate of possible water molecules that bind to the carbonyl oxygens of a solvent exposed helix. 
      dfnewxyz o c ca 0 0 0 t t t 2.93 122.1 23.0
      initial 
      write   sol.pdb 
           ; open an empty PDB file 
           ; to store the new coordinates
      ... (select solvent exposed helices)
      setenv tolower off
      seta HOH
           ; change the atom name in the text string 
           ; to HOH, which will be used for 
           ; the new record                
      newxyz

DFMAIN

Redefine main chain atom types.

Function: Definition, Information

Syntax:
1) DFMAIN
2) DFMAIN atom_1 [atom_2 ... atom_20]

Note:
The first form shows the current main chain definition.

See also: DFCA, MAIN, SHDF, SIDE and maximum number of atoms defined as main chain atoms.

Examples:
1) Define backbone atoms including Cb atoms as the main chain atoms. 

      dfmain n ca c o cb
2) Select N, Ca and C atoms 
      dfmain n ca c
      main

DFRES

Define atom order in a given residue and a single character name for that residue. This information is used by the SORT and SEQUENCE commands.

Function: Definition, Information

Syntax:
1) DFRES
2) DFRES res_type [:id] [(atom_names)]

Note:
1) The first form lists the current definition of residues.
2) EDPDB reads the DFRES definition from a file called pdbstd.dat in the current directory or in the edp_data: directory for the VMS version (or the edp_data/ for the unix version, when the information is needed.
3) The user's definition is always given priority over the definition read from the pdbstd.dat file.

See also: FILE, SEQUENCE, SHDF and SORT

Examples:
1) Define residue ALA. In the following example, the ala is the residue type to be defined, :a means that in a sequence file a residue of this type appears as a character a; and the following n ca c o cb are the five atom names that the residue ala should contain; it also indicates the order of the atoms appearing in a sorted list. 

      dfres ala :a n ca c o cb
2) Define residue SOL as anything. The default shortcut name is u which stands for Unknown. 
      dfres sol
3) List the current residue definitions 
      dfres
4) Make a pattern file of the hydrophobicity of the peptide. The :n stands for a non-polar residue, and :p stands for a polar residue. 
      dfres  ala :n
      dfres  asp :p
      dfres  cys :n
      ...
      dfres  tyr :n
      initial
      ca
      sequence hydr_patt.seq

SYMMETRY

Input one symmetry operator in the International Crystallography Table format.

Function: Definition, Information

Syntax:
1) SYMMETRY
2) SYMMETRY symmetry_operator
3) SYMMETRY PUNCH file_name [O]

Note:
1) The first form displays the current symmetry operators. The second form inputs one symmetry operator. The third form is similar to the first form, except a copy of the displayed symmetry operators will be written to a text file.
2) CELL parameter information is required to input symmetry operators. The symmetry information is accumulated with each input symmetry card. A CELL command initializes the symmetry information.

See also: CELL, MMIG, MOVECENTER, POLAR and SHDF

Examples:
1) Input the symmetry operators of space group P3(2)21. Each symmetry operator card includes the leading keyword SYMMETRY, and three character strings separated with space or comma from each other. 

      ! space group P3(2)21      
      symmetry x,y,z
      symmetry -y,x-y,z+2/3
      symmetry y-x,-x,z+1/3
      symmetry y,x,-z
      symmetry -x,y-x,-z+2/3
      symmetry x-y,-y,-z+1/3
2) Display the current symmetry information, including the symmetry operator number which is used to specify the operator in other commands (eg. MMIG). 
           symmetry
In the output, the operator marked with an asterisk can be used as an elementary operator, ie. all other operators can be created from a set of elementary operators. The ord information tell that how many times the operator needs to operate on itself to get a unitary operator. If an operator is labelled as the product of two other operators, it indicates that the operator has not been input and is listed just for information.

3) Use elementary symmetry operators to create the operators for the full space group. For example, the following commands create a file of symmetry operators of space group P6. 

      cell 100 100 100 90.0 90.0 120.0 1
      symmetry +y, -x+y, +z
      symmetry punch P6.edp
      cell , , , , , , ,
           ; initialize the SYMMETRY information
      @p6
           ; input the P6 symmetry operators
4) Create a P6 symmetry file for program 'O'. 
      cell 100 100 100 90.0 90.0 120.0 1
      @p6
      symmetry punch P6.sym o
Copyright 1995, Cai X.-J. Zhang, All Rights Reserved.