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cif2pdb

README for cif2pdb

Information for cif2pdb 1.0.1, 17 June 1998


program for conversion of an mmCIF data set to a pseudo-PDB entry
Version 1.0.1 17 June 1998

Herbert J. Bernstein
Bernstein+Sons
5 Brewster Lane, Bellport, NY 11713-2803
phone: 1-516-286-1999 email: yaya@bernstein-plus-sons.com

Frances C. Bernstein
Bernstein+Sons
5 Brewster Lane, Bellport, NY 11713-2803
phone: 1-516-286-1999 email: fcb@bernstein-plus-sons.com

For a discussion of the rationale behind this program, see cif2pdb: Translating mmCIF Data into PDB Entries

Work supported in part by IUCr (for HJB) and US NSF, PHS, NIH, NCRR, NIGMS, NLM and DOE (for FCB prior to 1998).

Before using this software, please read the
NOTICE
and please read the IUCr
Policy
on the Use of the Crystallographic Information File (CIF)

This program is available as a compressed shar cif2pdb.shar.Z (2.7 megabytes), a compressed C-shell shar cif2pdb.cshar.Z (2.7 megabytes) or as individual files, as given in the MANIFEST.

If your system cannot handle a Unix-style compressed file, you may wish to download an uncompressed shar cif2pdb.shar or an uncompressed cshar cif2pdb.cshar.

This program is version 1.0.1 of cif2pdb, a program for a conversion of an mmCIF data set to a partial pseudo-PDB entry with HEADER, TITLE, COMPND, SOURCE, KEYWRD, AUTHOR, JRNL, REMARK 1, REMARK 960, SEQRES, CRYST1, ORIGX, SCALE, ATOM, ANISOU, SIGUIJ (starting from U's or B's) HETATM, MASTER and END records. Fractional or orthogonal coordinates may be provided in the mmCIF data set. If an mmCIF dictionary or other dictionary with the necessary aliases between mmCIf and the core is provided, the program can convert core CIF data sets. This is sufficient to drive RASMOL.

Comments to yaya@bernstein-plus-sons.com appreciated.


WARNING

***** This directory contain files with the suffix ".pdb" Those files were produced by cif2pdb and are _not_ PDB entries.

SYNOPSIS

 cif2pdb [-i input_cif] [-o output_entry] [-d dictionary]
         [-p pdb_entry_id] [-f command_file] [-t u|l|p]
         [-m string_in_cif string_in_pdb] [[[input_cif]
         [[output_entry] [dictionary]]]
 input_cif defaults to $CIF2PDB_INPUT_CIF or stdin
 output_cif defaults to $CIF2PDB_OUTPUT_ENTRY or stdout
 dictionary defaults to $CIF2PDB_CHECK_DICTIONARY
 multiple dictionaries may be specified
  input_cif of "-" is stdin, output_entry of "-" is stdout
  -t has values of u for upper case, l for upper/lower,
    p for PDB typesetting codes, (default -t l)

COMPILATION

There are strong assumptions in the build of cif2pdb about the directory structure. cif2pdb is a ciftbx application. It is assumed that a current release of ciftbx is in a parallel directory. In order to avoid clobbering a prior version before you know this release of cif2pdb is working correctly in your system, it is assumed that you will unpack and build this package in a directory named

cif2pdb_1.0.1.

The resulting directory structure is then

                   top level directory
                   -------------------
                           |
           ----------------------------------
           |                                |
        ciftbx                        cif2pdb_1.0.1
        ------                        -------------
           |
      ciftbx.src
      ----------

In order to compile you will need a copy of ciftbx. In order to recreate the test output you will need a copy of the mmCIF dictionary. Compilation is controlled by Makefile, which may need changes for the target system. Changes can be made by editing Makefile, if necessary, but in most cases it is easier to edit the m4 document, Makefile.m4, and then

make Makefile_local

which will replace the current Makefile. Then cif2pdb can be compiled and tested by

make cif2pdb
make tests


Updated 17 June 1998

For further information contact Herbert Bernstein (yaya@bernstein-plus-sons.com)