Editing

Available commands: BLANK , PERMUTE , SET , SETA , SETB , SETC , SETE , SETI , SETR , SETT , SETW , UPDATE .

Editing commands modify the output fields, ie. text strings, W and B values, of the selected records. Specifically, every character in the text string can be modified. The editing commands listed below will not change the internal xyz coordinates (which may be used for geometry calculations).

BLANK

Blanks the x, y, z fields of the ON atoms.

Function: Editing

Syntax:
BLANK

Example: 1) To erase the x, y and z fields of the Ca atoms. 

      initial
      Ca 
      blank

PERMUTE

Permute columns in the text string of the ON atoms. PDB files output from different programs may have slightly different formats. For example, some fields may shift relative to each other. PERMUTE command can be used to fix this kind of problem by reformatting the record.

Function: Editing, Information

Syntax:
1) PERMUTE
2) PERMUTE i0 i1 shift

Note:
1) The first form outputs a ruler which defines the column number.
1) The i0, i1 are the starting and ending column numbers, respectively.
2) The shift is the number of times of one-character-permutations, which can be either positive or negative.

Examples:
1) To display the current test string and the column ruler. 

      zone all
      permute
2) Shift the residue number, which is currently at positions 16 - 19 of the text string, right-ward by one character. 
      permute 16 20 1
3) Shift the atom name, which is currently the at positions 8 - 10 of the text string, left-ward by two characters. 
      permute 6 10 -2
4) Reformat the record to switch the residue type (eg. Ala, Asp) at position 11 - 13 and the atom name at position 7-9. 
      permute 7 13 3
      permute 
           ; to check the result of the permutation.
           ; it does not look as expected
      permute 7 13 -3
           ; to restore the record, then try again
      permute 7 14 4
           ; or permute 6 13 4

SET

Set new text string etc. to all the ON atoms.

Function: Editing

Syntax:
SET (ATOM, RESIDUE, CHAIN, ID, WEIGHT, B, TEXT, ENTRY) parameters
Note:
The SET command duplicates the following SETx commands.
1) option ATOM -- SETA
2) option RESIDUE -- SETR
3) option CHAIN -- SETC
4) option ID -- SETI
5) option WEIGHT -- SETW
6) option B -- SETB
7) option TEXT -- SETT
8) option ENTRY -- SETE

See also: RESET and RTN

Examples:
1) Set chain name of the ON atoms to A 

      set chain A
2) Set the entry number for the ON records. 
      set entry

SETA

Set new atom name to all the ON atoms.

Function: Editing

Syntax:
SETA atom_name

See also: SET

Examples:
1) Change atom name from WT to HOH 

      initial
      atom wt
      seta hoh

SETB

Set the B-factor of the ON atoms to a given value or with the average B of the ON atoms of each residue.

Syntax:
1) SETB
2) SETB [b]

Note:
1) The first form sets the B factor to the average B of the ON atoms of each residue.
2) The second form sets the B factor to b, where -99.0 < b < 999.0.

See also: AVB and SET

Examples:
1) Set the B factors of the ON atoms to 25.0 

      setb 25.0
2) Set the B factors of side chain atoms to the average B of the side chain for each residue. 
      initial
      side 
      setb

SETC

Set new chain name to all the ON atoms.

Function: Editing

Syntax:
SETC [chain_name]

Note:
1) The chain_name is the new chain name (one character).
2) This command will not change the residue ID in the internal array (used for selection criterion), but will affect all the subsequent output (eg. LIST and WRITE commands).
3) If a chain_name is not input, SETC command will try to catch the last non-numeric character in the residue_id field of the text string of each ON atom, using it as the chain name, and erase the non-numeric characters from the residue_id field in the displayed text string.

See also: SET and SETI

Examples:
1) Set the chain name of the ON atoms to A 

      setc a
2) Set the chain name of the ON atoms to blank 
      setc ' '
3) Split the res_id in the text string into a chain name and a pure number. 
      setc

SETE

Set new entry number to the ON atoms in the current displaying order.

Function: Editing

Syntax:
SETE

See also: SET and SORT

Examples:
1) Reset the entry number after relabeling the atoms. 

      sort dfres
      sete
2) Use the entry number to indicate the B factor order. 
      zone all
      sort b  ; sort the records in an ascending B order.
      sete    ; set the entry number according the B order.
      sort    ; set the record order back to the original one.
      list    ; the entry number indicates the order of the B factors.

SETI

Set new residue_number (ID) to all the On atoms.

Function: Editing

Syntax:
1) SETI
2) SETI [new_res_# [incr_#]]

Note:
1) With the first form, SETI command will try to catch the last non-numeric character in the residue_id field of each ON atom, using it as the chain name. Note that the information comes from the residue_id, but not the text of the records.
2) With the second form, if the incr_# is specified, or the new_res_# is not an integer number, the residue_id field in the text string will be set to the new_res_#.
3) If both new_res_# and incr_# are integers, the residue_id field will be set to integer numbers starting from the new_res_# and increased by incr_#.

See also: SET and SETC

Examples:
1) Some programs punch out PDB files in which the chain name and the residue number are stacked together. To split them into two parts, type 

      seti
2) Set residue ID of the ON records to a100 
      seti a100
3) Set residue ID of the ON records to numbers starting from 401 and increased by 1. 
      seti 401 1

SETR

Set new residue type to all the ON atoms.

Function: Editing

Syntax:
SETR residue_type

See also: SET

Examples:
1) Set the residue_type of all the ON atoms to ALA. 

      setr  ala
2) Change the residue type of WAT residues to SOL 
      initial
      residue wat
      setr sol

SETT

Set new TEXT to all the On atoms.

Function: Editing

Syntax:
SETT column_1 column_2 text_stringg

Note: column_1 and column_2 are the starting and ending column numbers of the region where the text_string is to be written.

See also: PERMUTE, SET, TEXT, and UPDATE

Examples:
1) Set the atom name of the ON atoms to OH. 

      sett 7 10 'OH  '
           ; the same as seta oh
2) Set the Z field to blank. 
      permute
           ; check the column numbers for the Z field.
      sett 40 47 ' '

SETW

Set the W field of the ON atoms with a user specified value or a calculated value.

Function: Editing

Syntax:
1) SETW
2) SETW (wv, X, Y, Z, B, file_name) [(+W, -W, *W, /W)]

Note:
1) The first form sets the W field to res_#*0.1, where res_# is the residue order number in the input PDB coordinate file.
2) The wv is a real number to which the W column will be set. The option X, Y, Z or B will set the W column equal to the correspond column. The file_name specifies an acc.dat like file which defines the VDW radii for different types of atoms, and the W column will be set according the data in this file.
3) The options +W -W *W and /W can be used to modify the W value.

See also: ACCESS, AXIS, DISTANCE, SET and SWITCHWB Switch B and W columns. This command is useful for sharing EDPDB utilities between B and W columns.

Function: Editing

Syntax:
SWITCHWB

See also: AVB, RMSW, SETW and SUMW

Examples:
1) Switch the B and W columns. 

      switchwb
2) Calculate the average W for each residue. (Note that the value in the W field could be any real number). 
      switchwb 
      avb x   ; store the average W in 
           ; the X field of the CA atom for each residue.

UPDATE

Update the xyz, W or B fields of the ON records.

Function: Editing

Syntax:
UPDATE (XYZ, W, B) file_name fortran_format
UPDATE T column_1 column_2 file_name fortran_format [jump_after_string]

See also: SETT and SETW

Examples:
1) Change the xyz coordinates according to the data in a text file. 

      initial
      zone        all
      update      xyz new.dat '(3f8.3)'
2) Change the B factor of atom CA in residue 1 to 25.0 (on a vms system). 
      initial
      atom ca from {zone 1}
              ! or simply 'ca 1 ' 
      update      b  tt  (f10.0)
      10.0
              ! On VMS system, tt stands for the current terminal
3) Change column 22 to the secondary structure symbol defined by DSSP. The information is stored in a file called a.dssp and starts from the line after the text string ' #. 
	initial
	ca
	update t 22 22 a.dssp '(16x,a1)' ' #'
Copyright 1995, Cai X.-J. Zhang, All Rights Reserved.