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README for cif2pdb

Information for cif2pdb 2.0.3, 29 November 2009

Before using this software, please read the

and please read the IUCr

on the Use of the Crystallographic Information File (CIF)

This program is available as a compressed shar cif2pdb.shar.Z (3 megabytes), a compressed C-shell shar cif2pdb.cshar.Z (3 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 2.0.3 of cif2pdb, capable of doing 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, SIGATM, ANISOU, SIGUIJ (starting with 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. With version 2, the alternative of using WPDB format for output is provided, flagged by use of the -w option on the command line and in the output by the LEADER record in place of a HEADER record.

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]
         [-w yes|no] [-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)
 -w has the values yes or no (default -w no)

COMPILATION

There are strong assumptions in the build of cif2pdb about the directory structure. cif2pdb is a ciftbx application. It is assumed that cif2pdb.src is inserted in the ciftbx directory tree at the same level as ciftbx.src In order to avoid clobbering a prior version before you know this release of cif2pdb is working correctly in your system, you should save a copy of the current cif2pdb.src directory before unpacking this package.

The resulting directory structure should be

                   top level directory
                   -------------------
                           |
           ----------------------------------
           |               |                 |
        cif2pdb.src    ciftbx.src      dictionaries
        -----------    ----------      ------------

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 an appropriate 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

CHANGES

Release 2.0.3 adpated cif2pdb to the changes in CIFtbx for release CIFtbx 4.1.0

Release 2.0.2 incorporated improvements to the Makefile by G. Todorov to add a "make disclean" clause, correct an error in the definition of MMDICPATH, and add the entry for cif_mm_pdb2cif.dic to the dictionaries directory. The "make tests" clause was updated to include a timer. In order to improve timing, a counted string version of splitstr called csplitstr was created. instead of

Release 2.0.1 added support for WPDB format, corrected errors in the creation of REMARK 960 (and changed REMARK 960 to REMARK 9600 for the wide format), added the code for TITLE, SEQRES, FTNOTE and to handle anisotropic temperature factors from a separate loop. The changes for WPDB format include increases in the line length for the input CIFS to 2048 characters.

Release 1.0.2 corrected a error in the forming REF fields that caused some field to be truncated. Our thanks to Vince Stanev for isolating the problem. The duplicate upcase function was removed, since it is now in ciftbx.

Release 1.0.1 corrected the spelling of _atom_sites.fract_transf_matrix... and improved the handling of category keys.