Input/output

Available commands: APPEND , EXIT , LIST , READ , SEQUENCE and WRITE ,

As an editing program, EDPDB can output the editing result to either the terminal or to new PDB format files. It can also read multiple PDB files.

APPEND

Append the ON atom to an opened PDB format output file.

Function: Output

Syntax:
APPEND [comment]

Note:
The optional comment, which is usually a text string, will be written in front of the output records.

See also: WRITE

Examples:
1) Append the current ON atoms to the opened PDB file. 

      append
2) Switch the order of two molecules, A and B, in the output file. 
      initial
      chain b
      write ba.pdb 'REMARK molecule B the first'
      initial
      chain a
      append  'REMARK molecule A follows molecule B'

EXIT

Make an output a PDB file, and terminate EDPDB.

Function: Output, Control

Syntax:
EXIT [file_name] [(COS, HEADER, title )]

Note:
1) The default file name is the same as that of the (1st) input PDB file. To use the default file name, type a comma instead of a file name.
2) The default file type is .pdb.
3) The EXIT command is equivalent to a WRITE statement followed by a QUIT statement without the SAVE option.
4) See the documentation of the WRITE command for the information of the header options.

See also: QUIT and WRITE

Examples:
1) Write the current ON atoms to a new PDB file, and quit from EDPDB. 

      exit new_coor.pdb
2) Write a new PDB file including the cell parameter information, and quit from EDPDB. 
      cell 61.2 61.2 96.8 90.0 90.0 120.0 1 
           ; T4 lysozyme, P3221 crystal form
      exit new_t4l.pdb cos

LIST

List the ON atoms on the terminal.

Function: Output

Syntax:
1) LIST [ n1 [n2] ] 2) LIST ZONE 3) LIST VECTOR [dmin, dmax, max_center_to_center_dist]

Note:
1) The n1 and n2 are the sequential numbers of the sorted ON records, which between which the records will be listed.
The default of n1 is 1, and the default of n2 is the end of ON atoms.
2) The second form lists the currently selected zone(s).

See also: SORT and WRITE

Examples:
1) List all the ON atoms. 

	list
2) List the 100th-110th Ca atoms. 
	initial
	Ca
	list 100 110
3) List the 1500th ON atom and its following atoms. 
	list 1500
4) List the top 40 best ordered solvent molecules, ie the solvent molecules of the lowest B factors. 
	initial
	residue sol
	sort b
	list 1 40
5) List the residues that are within 4.5 A from OG atom of residue 16. 
	initial
	nayb 4.5 16 OG
	list zone
6) List the topology of the beta sheets. (Ref. Koch, et al. (1992). Analysis of Protein Sheet Topologies by Graph Theoretical Methods. Protein: Struc., Func., and Gen.. 12:314-323). 
	initial
	.... ; selete beta strands
	list vector

READ

READ the ATOM records from an existing PDB file.

Function: Input

Syntax:
READ file_name [mark] [INITIALIZE]

Note:
1) The mark is a character string, which will be used to substitute the chain names in the input file. (See Start EDPDB for more information).
2) If the INITIALIZE option is used, the original records stored in the program will be overwritten. Otherwise, the new records will be appended to the original ones.
3) The file input with a READ command can not be recovered with the RESET command.

See also: RESET and Start EDPDB

Examples:
1) Read a PDB file, keep the chain name as it is, and overwrite the previously input records. 

      read  file_b.pdb  ,  initialize
  or
      read  file_b.pdb  _  initialize
2) Read a PDB file (abcd.pdb) which contains A, B, C and D four chains. The chain names will be changed to S, T, U and V when they are read in. 
      read  abcd.pdb stuv

SEQUENCE

Create an output file containing the single character sequence of the selected residues. The three character to one character change is based on the information input with the DFRES command or the pdbstd.dat file.

Function: Output

Syntax:
SEQUENCE [file_name] [format] [C]

Note:
1) The file_name defines an output file name for the sequence. The default file name is the input file name with a .seq file type.
2) The format is a FORTRAN output format for output of the sequence characters. The default format is (5(1X,10A1)).
3) If the optional C is used, the chain name of the first ON atom of each residues will be output as the sequence characters.

See also: DFRES, FILE and SETC

Examples:
1) Output the amino acid sequence of residues 1 - 164 to a file called aa.seq. 

      zone 1 - 164
      sequence aa.seq
2) Output the burial-solvent_exposure pattern of the protein molecule. 
      initial
      ca
      setc b
           ; B stands for burial, to initialize with
      more
      access
      sumw x
           ; calculate the solvent accessible area of each residue    
      initial
      ca from { x > 20.0 }
           ; select solvent exposed residues
      setc E  ; E stands for exposed 
      ca
      sequence pattern.seq

WRITE

Make a new file to output the current ON atoms. The file will remain opened and APPEND-able until is CLOSEd. The WRITE command also automatically closes the previous output PDB file if exists.

Function: Output

Syntax:
WRITE file_name [(COS, HEADER, BLANK, title )] [format]

Note:
1) The default file type of the output file is .pdb. The VMS EDPDB always creates a new-version file of the specified filename, while the unix one overwrites the old file of the specified filename if it exists.
2) If the option COS is used, the CRYST, ORIGX and SCALE information will be written onto the new PDB file. This is the default option if the required cell parameters have been input.
3) If the option HEADER is used, the header from the 1st input PDB file will be copied to the new file.
4) BLANK option is used to superess any header output. It becomes the default option if on cell parameter has been input.
5) The title is a text string that is enclosed with a pair of quotation mark (' '). It will be output before other records.
6) The format must be a FORTRAN output format for a text string and two real numbers. It can be used to reformat the output records. The default is the PDB format.
7) The order of the output records can be affected by the SORT command.

See also: APPEND, CELL, CLOSE, CLOSER, MMIG, READ, SHAPE and SORT

Examples:
1) Output the Ca atoms to a PDB file, eg. called Ca.pdb 

      initial
      ca
      write Ca.pdb
2) Output the ON atoms to a PDB file and add the CRYST, ORIG and SCALE information. 
      cell 61.2 61.2 96.8 90.0 90.0 120.0 1
      write new_coor.pdb cos
3) Output the ON atoms to a PDB file and copy the header from the original (1st) input PDB file. 
      write new_coor.pdb header
4) Output the ON atoms to a PDB file and add a title to the PDB file. Note that the double quotation mark is to prevent changing the title to lower cases. 
      setenv tolower off
      write new_coor.pdb 'REMARK This is a test PDB file.'
5) Output the ON atoms to a file in which the W, B column is at the beginning of each record. 
      write new_coor.dat , '(t20,a,t1,2f8.3)'
Copyright 1995, Cai X.-J. Zhang, All Rights Reserved.