CHANGES.html

Version History

2.4.2 6 Oct 2004 -- H. J. Bernstein

1. Fixed misaligned loops for SEQADV and MODRES translation. Bug reported by dust@iwonka.med.virginia.edu.

2.4.1 21 Sep 2004 -- H. J. Bernstein

1. PDBX_POLY_SEQ_SCHEME tokens added to link sequence to atom list.

2.3.9 17 Apr 2000 -- Helge Weissig (via HJB)

1. Fix y2K bug (add 100, not 1000 for years before 70.

2.3.8 30 May 2000 -- H. J. Bernstein

1. Increase number of footnotes from 9 to 999 to correct problem reported by Jurgen F. Doreleijers.
2. Fix typos in comments.
3. Add new flag, use_pdb2cif_prefix defaulted to value of m4 macro USEPREFIX to control use of pdb2cif prefix.
4. Rework verbose tags to include new tags in pdb2cif_cif_mm_0.0.05.dic.
5. Upgrade to _atom_site.pdb2cif_label_model_is and add _atom_site.pdb2cif_id_in_model, _atom_site.pdb2cif_auth_id_in_model to ATOM_SITE category. Rework atom serial number logic to recognize entires with repeated serial numbers and produce unique _atom_site.id values. Allow for 999,999,999 atoms.
6. Rework warning messages to avoid going past column 80 with long tags.

2.3.7 7 March 1999 -- H. J. Bernstein

1. Update email address for pdb2cif bug reports, and update pdb2cif JAC reference.
2. Convert atom type and charge with non-standard information to standard form.
3. Process special UNK SEQRES records
4. Start changing years to 4 digits in comments
5. Make sequence alignment more robust for cases reported by Steve Brenner. Make 4 passes, avoid short sequence matches for the first three and limiting segment to segment discontinuities, especially for portions of chain which are connected in the ATOM list.
6. Change all WARNING message to begin with the string "# **** WARNING" and important summary diagnostics to begin with "#=#".
7. Fix "%%" to "%%%%" in ENTITY_POLY_SEQ summary message.

2.3.6 15 June 1998 -- H. J. Bernstein

1. Correct address and email information for FCB.
2. Update related comments.

2.3.5 3 May 1998 -- H. J. Bernstein

1. Correct handling of long references.
2. Correct handling of JRNL PUBL records.
3. Update comments for support and JAC reference.
4. Change quote mark on residue names.

2.3.4 12 Oct 1997 -- H. J. Bernstein

1. Correct handling of two blank fields in SEQADV.
2. Correct typos in STRUCT_MON_PROT tags.

2.3.3.2 7 Aug 1997 -- H. J. Bernstein

1. Correct spurious secondary struture headers when ssbond records are present without any secondary structure.

2.3.3.1 5 June 1997 -- H. J. Bernstein

1. Minor revisions to the Web pages.
2. URLs in comments in the program updated.
3. Changes made in the m4 script for the gnu m4 handling of format.

2.3.3 27 Jan 1997 -- H. J. Bernstein

2. Corrections to comments to update URLs.
1. Change _citation.journal_coden_ASTM to _citation.journal_id_ASTM
2. Change _citation.journal_coden_ISSN to _citation.journal_id_ISSN
3. Change _citation.journal_coden_CSD to _citation.journal_id_CSD
4. Change _citation.book_coden_ISBN to _citation.book_id_ISBN
5. Change _diffrn_radiation.wavelength tokens to _diffrn_radiation_wavelength tokens
6. Change _diffrn_radiation.detector tokens to _diffrn_detector tokens
7. Change _diffrn_radiation.source tokens to _diffrn_source tokens
8. Change _diffrn_refln.crystal_id to diffrn_refln.diffrn_id
9. Add new _reflns tokens
10. Change _atom_sites.frac_.. tokens to _atom_sites.fract_ tokens

2.3.2 22 Sep 1996 -- H. J. Bernstein

1. Include standard residues used in entry in CHEM_COMP to satisfy dictionary parent/child relationships.
2. Add _symmetry.entry_id to provide required key for SYMMETRY category.
3. Map all _exptl.method to lower case and map "x-ray diffraction" to "single-crystal x-ray diffraction" to improve dictinary compliance. Add warnings for values which are not in dictionary enumeration of acceptable values.
4. Protect against missing PDB entry coden.
5. Change journal volume field to 4 characters.
6. Default publications with neither and ISSN nor an ISBN to be treated as books, unless they have a volume or are "TO BE PUBLISHED".
7. Add _reflns.entry_id to provide required key for REFLNS catgeory. Ensure against duplication in verbose mode.
8. Change "TURN" to "TURN_P" for compliance.
9. Change _atom_site.auth_aym_id value from " " to a period for compliance.
10. Give the entity id number instead of the three letter code for _entity_name_com.entity_id.
11. Move _database_PDB_rev.date_original into loop.
12. Fix duplicated site information.
13. Move _publ_manuscript_incl.entry_id into loop.

2.3.1 24 Aug 1996 -- H. J. Bernstein

1. Test for volume = 1 and NMR entries.
2. Report unusual B-values or occupancies on NMR entries.
3. Handle empty field and miscount from split on some older versions of perl when doing a slip on a blank line.
4. Handle versions of perl which don't support scalar localtime.
5. Correct order of author names in one comment.

2.3.0 24 Jul 1996 -- H. J. Bernstein

1. Report CSD codens on references.
2. Fixed truncated publication names.
3. Correct type of DBREF sequence information.
4. Make ISSN, ISBN use consistent.
5. Allow for doubled up sequence database citations

2.2.7 12 Jun 1996 -- H. J. Bernstein

1. Correct format of ATOM_SITE data items when processing February 1996 V 2.0 PDB format.
2. Change from ENTITY_NAME_SYS to ENTITY_NAME_COM for HETNAM, HETSYN

2.2.6 12 May 1996 -- H. J. Bernstein

1. Add code for CISPEP, tokens _struct_mon_prot.label_model_id, _struct_mon_prot_cis.label_model_id
2. Add code for HYDBND, SLTBRG, LINK
3. Add code for SIGUIJ, SIGATM
4. Add code for MODRES
5. Add code for END
6. Reorganize code to be more readable
7. Correct het_site_text to columns 31-70
8. Save memory for insertion codes by combining with seq number

2.2.5 5 May 1996 -- H. J. Bernstein

1. Fix error in perl/oawk handling of dotoupper, dotolower macros.
2. Add flag for compliance_level to control processing for February 1996 PDB format.
3. Add preliminary code for HETSYN and HETNAM, and pick up name from HET.
4. Improve determination of atom type from atom name, matching types against FORMUL (for HETS) or H, D, C, N, O, P, S for standard residues, or the periodic table, if necessary.
5. Fix error in awk/oawk handling of record types such as CONECT or HETATM which may merge with a following atom number.
6. Add _entry.id, _database_pdb_matrix.entry_id, _atom_sites.entry_id, cell.entry_id to dataset.
7. Add warning that REMARKS are stripped to columns 12-70.
8. Align spacing for multiple model atom lists, and create space for segment id's.
9. Add new tokens _struct_conn.ptnr1_atom_site_id and _struct_conn.ptnr2_atom_site_id to list atom_site.id's with structural connectivity.

2.2.4 25 Apr 1996 -- H. J. Bernstein

1. Add processing of MODEL to _atom_site.label_model_id
2. Correct error in naming of nHxx atoms
3. Move major comment heading to end of file and provide clear disclaimer
4. Report more sequence homology mismatch of less than 90 percent for more cases
5. Suppress resolution line when no data
6. Report non-standard token use with PUBL_MANUSCRIPT_INCL if MODEL or SEQADV are used.

2.2.3 18 Mar 1996 -- H. J. Bernstein

convert to _database_pdb_tvect...

2.2.2 18 Mar 1996 -- H. J. Bernstein

convert to _struct_ncs_oper.code

2.2.1 12 Mar 1996 -- H. J. Bernstein

1. add ...label_seq_num tokens to comply with mandatory status
2. change HELX_2_7 to HELX_27
3. correct handling of residue numbers in SITE
4. relocate CONNECT and SSBOND code to run after sequence number processing

2.2.0 9 Mar 1996 -- H. J. Bernstein

Conversion or version 0.8.0 of cifdic.m96 of 6 Mar 1996
1. Use _struct_ncs_oper... for MTRIX
2. Change ...coden_PDB to ...coden_CSD
3. Change _atom_site.label_seq_num to _atom_site.auth_seq_num
4. Change _atom_site.entity_id to _atom_site.label_entity_id
5. Change all miscellaneous ...label_seq_num tokens to ...auth_seq_num
6. Change entity_reference... to struct_ref...
7. Change entity_poly_seq_dif ... to struct_ref_seq_dif
8. Add code for TVECT as database_pdb_matrix.tvect...

2.1.3 1 Mar 1996 -- H. J. Bernstein

Changed chem_comp.mon_nstd_flag for non-polymeric HETs from "no" to "."

2.1.2 22 Feb 1996 -- H. J. Bernstein

Fix item count for blank volume and/or country

2.1.1 22 Feb 1996 -- H. J. Bernstein

1. Fix erroneous use of semi-colon in jrnl_pub ...
2. Fix Space Group
3. Fix error in sheets causing a loop miscount when no hydrogen bonds for registratioon are given. (Thanks to P. Keller for spotting this).

2.1 1 Feb 1996 -- H. J. Bernstein

Changes for 31 Jan 1996 mmCIF dictionary and recent mailing list clarifications
1. Keep Junior, Senior etc with last name

2. Comment out TERs

3. Update comments

1.1.3-beta 25 Jan 1996 -- H. J. Bernstein

1. Invert Author names

2. Allow embedded redefinitions of verbose, etc.

1.1.2-beta 21 Jan 1996 -- H. J. Bernstein

1. Fix erroneous report of no homology on very short chains.

2. Fix error in spelling and use of auth_convtext

3. Fix digit range on sequence signatures

4. Summarize all warnings in comments at end

5. Pad all lines to 80 characters

6. Code for DBREF and SEQADV

7. Fix code for OBSLTE and SPRSDE

8. Clean up a lot of spacing

9. Try to match PDB reference numbers, if possible

10. Removed indications of donor, acceptor, positive, negative from connectivity, since PDB no longer identifies these roles

1.1.1-beta 8 Dec 1995 -- H. J. Bernstein

1. List all struct_asym.id's

2. Remove leading digits from atom names

3. Remove use of _chemical.name_common for COMPND and map COMPND, TITLE, SOURCE and CAVEAT to _struct.title

4. Fix expdta format.

5. Move first author back into general author list

1.1.0-beta 2 Dec 1995 -- H. J. Bernstein and F. C. Bernstein

1. Assign blank chain-id to "*" or ".", with "*" used for ATOM and TER and, if there is only one chain for HETATM

2. Correct ssbond comment handling

3. Provide control of AUTH/EDIT typesetting with auth_convtext

1.0.11-alpha 1 Dec 1995 -- H. J. Bernstein

1. Minor cleanup and flag untranslated lines

2. Cleanup remaining non-mmCIF names except for open MTRIX questions.

3. Correct handling of KEYWDS/KEYWRD for split keywords

1.0.10-alpha 11 Nov 1995 - H. J. Bernstein

1. Converted from awk script to m4 document which is used to produce awk variations and perl script

2. correct ..._res_id to _comp_id in bonds

1.0.9-alpha 2 Nov 1995 -- H. J. Bernstein

Adopt cell.Z_PDB instead of cell.formula_units_Z

1.0.8-alpha 30 Oct 1995 -- H. J. Bernstein

Fix volume calculation

1.0.7-alpha 29 Oct 1995 -- H. J. Bernstein

1. Add clear warnings about limitations

2. Fix _atom_site.entity_seq_num information for the case of disordered residues presented non-interleaved, as in 5hvp

3. Start conversion to m4 for old awk versions

4. Add conditional code to put entity_seq_num info into all atom sites where known, provided dense_list is not "yes"

1.0.6-alpha 26 Oct 1995 -- H. J. Bernstein

Sequence matching

1.0.5-alpha 10 Oct 1995 -- H. J. Bernstein

1. Rework of formul and SEQRES

2. Make "covale" " . " for bonds, since PDB does not distinguish bond orders any more

3. Fix gawk'ism in SHEET

1.0.4-alpha 19 Oct 1995 -- H. J. Bernstein

1. Fix extraneous output from REVDAT

2. Add warning comments about gawk and date

3. Fix handling of saltbr and exptl.method

1.0.3-alpha 13 Oct 1995 -- H. J. Bernstein

1. Revise sheet handling to match current dictionary

2. Convert ORIGX to cifdic.m95 0.7.28 (6 Oct 1995) definition

1.0.2-alpha 6 Oct 1995 -- H. J. Bernstein

Many more changes of item.id's and added first pass at typesetting codes, controlled by convtext="yes"

1.0.1-alpha 29 Sep 1995

fix Phil's email address. -- HJB

1.0-alpha 28 Sep 1995

base version of mmCIF cifdic.m95 version
in a state ready for testing. Makes some assumptions about handling of ORIGX, MTRIX and TER which are not settled in mmCIF, and may need to be changed. There are still several PDB record types to be translated, and the ordering of the output needs to be improved.
Herbert J. Bernstein, Bernstein+Sons
yaya@bernstein-plus-sons.com

1. Reorganized SCALE, MTRIX, ORIGX to common
format.

2. Added handling of KEYWRD, OBSLTE, SPRSDE

3. Reorganized atom site list and included TER

4. Reorganized FTNOTE output and moved down in output

0.9c-mm-alpha 23 Sep 1995

corrected handling of formulas and id's of HETs

0.9c-mm-pre-alpha 22 Sep 1995

Based on mmCIF dictionary v0.7.24 31 Aug 1995, cifdic.m95, 22 September 1995, HJB, B+S

1. Automatically converted all official aliases in version 0.9c, including most in comments to standard mmCIF names

2. Manually converted most of the rest

3. Revised handling of ANISOU to use the necessary atom_site category items with
lines embedded in the loops if ANISOU cards are present.

4. Revised REVDAT handling to print at the end of processing, using "_database_pdb_rev"
and "_database_pdb_rev_record" loops

5. Changed the atom types to the first 2 characters of the PDB atom name

6. Squeezed out the blanks from the middle of PDB atom names to remove the need for quote marks

7. Changed " " default chain indicators to "." instead of "A", since "A" could cause mis-assignments

Prior Versions by P. Bourne

0.9c Nov 1993 Based on mmCIF dictionary v0.5, 01-sep-1993

1. Added _data block designator based on filename

2. Quoted space group ie 'P21 21 21'

3. All references to _atom_id are now in quotes to avoid N A ie atom names in HETS containing white space.

4. MTRIX fixed - field spec. wrong in Guide to Author wrong number of items - fixed

5. H-M should be H_M in space group name - fixed.

6. Removed some of the keyword dependencies e.g. will now process list of ATOM only records

7. Handling of book citations in JRNL and REMARK 1 fixed.

0.9b Sept 1993 Based on mmCIF dictionary v0.5, 01-sep-1993

1. Reworked the handling of _entities

2. Added the verbose option.. this is useful if you intend using the converted file as a template for bigger and better things

3. Corrected a number of loop_ problems

4. Added new data items to the following:
_diffrn_*
_struct_asym_*
_entity_reference_*
_entity_nonp_*
_entity_mon_*
5. Corrected _struct_conf_id

0.9a Sept 1993 Based on mmCIF dictionary v0.5, 01-sep-1993

1. Much faster by storing not only incremental atom info. but also PDB atom numbering info for use by CONECT records

2. Added _atom_sites_alt_id _atom_sites_alt_details

3. Added _struct_conn_par1_label_alt_id and _struct_conn_par2_label_alt_id

4. Added _struct_site_gen_label_alt_id

5. Added "_database_PDB_rev_replaces"