README for cif2pdb INFORMATION FOR CIF2PDB 0.3.1, 26 OCTOBER 1997 _________________________________________________________________ program for conversion of an mmCIF data set to a pseudo-PDB entry Version 0.3.1 26 October 1997 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 Protein Data Bank Biology Department, Brookhaven National Laboratory, Upton, NY 11973-5000 phone: 1-516-344-2261 email: bernstei@bnl.gov 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 under contract DE-AC02-76CH00016 (for FCB). _________________________________________________________________ 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 a preliminary version capable of doing a conversion of an mmCIF data set to a partial pseudo-PDB entry with HEADER, TITLE, COMPND, SOURCE, SEQRES, CRYST1, ORIGX, SCALE, ATOM, HETATM, MASTER and END records. Version 0.1.0 added KEYWRD, AUTHOR, JRNL, REMARK 1 and REMARK 96. This is sufficient to drive RASMOL. Version 0.2.0 added ANISOU, SIGUIJ starting from U's or B's in the ATOM_SITE list (not ATOM_SITE_ANISOTROP) Version 0.2.1 changed REMARK 96 to REMARK 960. Version 0.3.0 corrected a duplicate declaration of the variable TAG, and initialized a previously uninitialized bookmark. Version 0.3.1 corrected two problems related to dictionary use. First, the type of residue numbers was not being properly recognized when pure numeric residues were used. Second, various numeric fields in REMARK 960 were spuriously flagged as incorrectly typed. Both problems have been fixed. In addition, the Makefile has been cleaned up and reorganized. 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_0.3.1. The resulting directory structure is then top level directory ------------------- | ---------------------------------- | | ciftbx cif2pdb_0.3.1 ------ ------------- | 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 2 November 1997 For further information contact Herbert Bernstein (yaya@bernstein-plus-sons.com)