PDBGET(L)		  CSDS Commands			PDBGET(L)

NAME
     pdbget - retrieve PDB files from the CSD PDB CD-ROM

SYNOPSIS
     pdbget [ -f code_file ] [ -o output_file ]	[ -p  search_path
     ] [ -dir directory	] [ -strip string ] [ -c ] [ -d	] [ -dl	]
     [ -lower ]	[ -l ] [ -h ]

DESCRIPTION
     pdbget copies PDB files from the Cambridge	 Structual  Data-
     base  PDB	CD-ROM	to  writable  file.  Individual	files are
     referenced	by their 4 character PDB codes.	(e.g. 1ycc).

OPTIONS
     -f	code_file
	  Read PDB 4 character codes from file code_file. If  not
	  specified pdbget reads from standard input.

     -p	 search_path
	  Use the search path search_path instead of the environ-
	  ment	 variable  CSDPDBFILESEARCHPATH	 to  resolve  PDB
	  filenames.

     -l	   Lower the case of all  input	 brookhaven  4	character
	  codes	before processing.

     -h	   Print a short help message

     -d	   Decompress the files. pdbget	will use gzip or compress
	  to  uncompress the PDB files before writing them to the
	  target files.

     -dirdirectory
	  Directory in which to	store output files.  Defaults  to
	  current directory.

     other options....

     -o	output_file
	  Write	files to file  output_file  instead  of	 standard
	  output.  Only	 effective  with  the	- c concatenation
	  option. Ignores the -dir directive.

     -dl   as for -d above but don't attempt to	strip off the  .Z
	  or .gz extensions.

     -c	   Concatenate all input files together.

     -lower
	  convert all output filenames to lower	case.

     -strip string

CSD System  Last change: $Date:	1998/01/14 09:56:22 $		1

PDBGET(L)		  CSDS Commands			PDBGET(L)

	  Strip	the character string string off	the end	of  every
	  output filename.

ENVIRONMENT
     pdbget recognises	the  environment  variables  CSDHOME  and
     CSDMACHINE.  (see	quest(l)).  In addition	it recognises the
     environemnt variables

     CSDPDBHOME
	  Name of the root directory containg the PDB files.

     CSDPDBFILESEARCHPATH
	  Specfies a colon separated list of filenames to  search
	  when	resolving the PDB 4 character codes.  Defaults to
	  the string
	  %h/distr1/%s/pdb%n.%e.gz:%h/distr2/pdb%n.%e.gz:%h/distr1/%s/pdb%n.%e.gz.
	  Given	 a particular 4	character code pdbget will search
	  the files specifed by	CSDPDBFILESEARCHPATH string  sub-
	  stituting for	the following if they occur:
	  %h =>	the value of the environment variable CSDPDBHOME.
	  %H =>	upper case of the value	of the	enviromnet  vari-
	  able CSDPDBHOME.
	  %n =>	4 character PDB	code
	  %N =>	upper case of 4	character PDB code
	  %s =>	middle two characters of 4 character pdb code
	  %S =>	upper case of middle two charcters of 4	character
	  PDB code
	  %e =>	the string "ent" if  the  4  character	PDB  code
	  begins with 1	or "noc" if it begins with 0.
	  %E =>	the string "ENT" if  the  4  character	PDB  code
	  begins with 1	or "NOC" if it begins with 0.
	  %v =>	the first character of the 4 character PDB code.
	  %V =>	upper case of the first	character of the 4  char-
	  acter	PDB code.
	  %a =>	the second character of	the 4 character	PDB code.
	  %A =>	upper case of the second charcter of the 4  char-
	  acter	PDB code.
	  %b =>	the third character of the 4 character PDB code.
	  %B =>	upper case of the third	charcter of the	4 charac-
	  ter PDB code.
	  %c =>	the fourth character of	the 4 character	PDB code.
	  %C =>	upper case of the fourth charcter of the 4  char-
	  acter	PDB code.

EXAMPLES
     If	the CD-ROM is mounted without the  Rock-Ridge  extensions
     then   the	  PDB	filenames   will   appears  in	the  form
     DISTR1/YC/PDB1YCC.ENT;1. To correctly obtain  the	file  set
     CSDPDBFILESEARCHPATH to be	the string
     %h/DISTR1/%S/PDB%N.%E;1:%h/DISTR2/%S/PDB%N.%E;1:%h/DISTR3/%S/PDB%N.%E;1
     and use the command
     pdbget -dl	-lower

CSD System  Last change: $Date:	1998/01/14 09:56:22 $		2

PDBGET(L)		  CSDS Commands			PDBGET(L)

     to	get a decompressed file	called pdb1ycc.ent in the current
     directory.

SEE ALSO
     The "Unix Installation Notes", CCDC.

CSD System  Last change: $Date:	1998/01/14 09:56:22 $		3