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The major steps needed to translate mmCIF data into a "pseudo-PDB" format (a format sufficiently similar to standard PDB format to be accepted by most applications) are presented, with examples drawn from the program cif2pdb [BB96]. The objective is to help application developers and people writing CIFs understand uses of mmCIF which will hinder translation to PDB format and to help users familiar with PDB format understand new mmCIF constructs.
The Protein Data Bank format [PDB77, PDB95, PDB96] has been used for over 20 years to archive macromolecular data, is produced by many refinement programs and is used as an input format by many applications. Adoption of the mmCIF dictionary [FBB96] by the IUCr will lead to the creation of a significant pool of mmCIF data sets. However, it may be some time before existing application programs can handle mmCIF input. Therefore it is important to have facilities to translate mmCIF data into PDB format to facilitate the use of CIFs with existing programs. The PDB is developing a CIF-based AutoDep program [SAMXS96] ,which uses the WWW. In those areas where there is a one-to-one correspondence, AutoDep will use mmCIF tokens and produce the appropriate PDB records. However, there are areas where more complex transformations are needed and in user labs it is not always possible, or even desirable, to make a perfect PDB entry from an mmCIF data set. If the only purpose of the translation is to display a molecule, then there may be no reason to reorganize residues and het groups and change atom names to match PDB standards. We discuss both the production of a "pseudo-PDB" format which can be converted into a rigorous PDB format with further processing, and the capabilities of the PDB AutoDep program. We consider ways to construct a valid PDB ATOM/HETATM/TER list, and approaches to deal with mmCIF tag values for chain identifiers and atom names which may not fit into PDB field sizes.
A simple tabular concordance can be used for some tokens, and portions
of such a concordance
are presented. Much of the work of translation from PDB format to mmCIF
format has
been automated, though careful checking of the results is required and
considerable manual revision is necessary for some entries. Work on
automated translation from
mmCIF format to PDB format is in progress. The status of the program
cif2pdb[BB96] is presented.
The PDB format and mmCIF are different both in presentation and in content. The PDB format consists mainly of fixed format fields in an ordered set of records. The new mmCIF format is one of a family of STAR (Self-Defining Text Archive and Retrieval File [HS94]) formats which uses a tag-value style of presentation and has very little sensitivity to the ordering of the information. The content of PDB entries is organized around the presentation of sets of atomic coordinates associated with chains and HET groups. Some of the PDB record types have a very broad scope, drawing on data from many distinct conceptual levels. The content of mmCIF data sets is organized around "entities" (discrete chemical components). In most cases the data is broken down into tables oriented towards a single conceptual level. With care, all the information of interest about a macromolecule can be presented in either format clearly and efficiently, but challenging problems arise in moving between the two formats. When moving from mmCIF to PDB format, the fixed fields of the PDB format limit the range of values they may hold. Structural features identified in mmCIF in terms of entities and relative position within a sequence need to be re-identified in terms appropriate to PDB format. Separate mmCIF tables need to be joined to bring together the information needed for some PDB record types.
mmCIF [FBB96] uses a system of tags and values to describe a structure, as
shown in the extract
giving the chain sequences from the pdb2cif conversion of PDB entry
4INS [DHH89]:
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
1 1 GLY 1 2 ILE 1 3 VAL 1 4 GLU 1 5 GLN
1 6 CYS 1 7 CYS 1 8 THR 1 9 SER 1 10 ILE
1 11 CYS 1 12 SER 1 13 LEU 1 14 TYR 1 15 GLN
1 16 LEU 1 17 GLU 1 18 ASN 1 19 TYR 1 20 CYS
1 21 ASN
2 22 PHE 2 23 VAL 2 24 ASN 2 25 GLN 2 26 HIS
2 27 LEU 2 28 CYS 2 29 GLY 2 30 SER 2 31 HIS
2 32 LEU 2 33 VAL 2 34 GLU 2 35 ALA 2 36 LEU
2 37 TYR 2 38 LEU 2 39 VAL 2 40 CYS 2 41 GLY
2 42 GLU 2 43 ARG 2 44 GLY 2 45 PHE 2 46 PHE
2 47 TYR 2 48 THR 2 49 PRO 2 50 LYS 2 51 ALA
Because tags are always given, the same information can be presented in
different
orderings. The Protein Data Bank [PDB96] uses a format with fixed fields
and is order-dependent.
Here is the sequence information from the PDB entry:
SEQRES 1 A 21 GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU 4INS 170 SEQRES 2 A 21 TYR GLN LEU GLU ASN TYR CYS ASN 4INS 171 SEQRES 1 B 30 PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU 4INS 172 SEQRES 2 B 30 ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR 4INS 173 SEQRES 3 B 30 THR PRO LYS ALA 4INS 174 SEQRES 1 C 21 GLY ILE VAL GLU GLN CYS CYS THR SER ILE CYS SER LEU 4INS 175 SEQRES 2 C 21 TYR GLN LEU GLU ASN TYR CYS ASN 4INS 176 SEQRES 1 D 30 PHE VAL ASN GLN HIS LEU CYS GLY SER HIS LEU VAL GLU 4INS 177 SEQRES 2 D 30 ALA LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE PHE TYR 4INS 178 SEQRES 3 D 30 THR PRO LYS ALA 4INS 179
The major differences in syntax are as follows:
PDB and mmCIf formats agree simply and directly for some data items, such as cell parameters, and admit a simple tabular mapping, as shown by this extract from the concordance [B96] which is available as part of pdb2cif [BBB97]:
PDB Field Content Type of Transformation
and Related mmCIF field
CRYST1[1-6] CRYST1 NA
CRYST1[7-15] a equivalent to _cell.length_a
CRYST1[16-24] b equivalent to _cell.length_b
CRYST1[25-33] c equivalent to _cell.length_c
CRYST1[34-40] alpha equivalent to _cell.angle_alpha
CRYST1[41-47] beta equivalent to _cell.angle_beta
CRYST1[48-54] gamma equivalent to _cell.angle_gamma
CRYST1[56-66] sGroup equivalent to
_symmetry.space_group_name_H-M
CRYST1[67-70] z equivalent to _cell.Z_PDB
while other important macromolecular data descriptors, because
of the very different views of the same data,
require complex transformations.
For example, in mmCIF, sheets are built up out of strands. All the strands in all sheets are listed in one STRUCT_SHEET_RANGE table. The relative ordering and orientation of all strands in all sheets are given in one STRUCT_SHEET_ORDER table. The hydrogen-bonding among all strands in all sheets is listed in one STRUCT_SHEET_HBOND table. The general characteristics of all sheets per se is given in one STRUCT_SHEET table. To convert to PDB format all these separate tables must be joined and the information extracted in terms of simple, nonbifurcated sheets, one order-dependent table per nonbifurcated sheet with each row carrying the definition of a strand, orientation and partial hydrogen-bonding relative to the prior strand in the same table.
Here is the strand information from a CIF of 2ACE [HRSS96] in mmCIF format.
loop_ _struct_sheet.id _struct_sheet.number_strands #-------#-------#-------#-------#-------#-------#-------#-------#-------#----- #id #number_strands A 3 B 11 loop_ _struct_sheet_hbond.sheet_id _struct_sheet_hbond.range_id_1 _struct_sheet_hbond.range_id_2 _struct_sheet_hbond.range_1_beg_label_seq_id _struct_sheet_hbond.range_1_beg_label_atom_id _struct_sheet_hbond.range_2_beg_label_seq_id _struct_sheet_hbond.range_2_beg_label_atom_id _struct_sheet_hbond.range_1_end_label_seq_id _struct_sheet_hbond.range_1_end_label_atom_id _struct_sheet_hbond.range_2_end_label_seq_id _struct_sheet_hbond.range_2_end_label_atom_id #-------#-------#-------#-------#-------#-------#-------#-------#-------#----- #sheet_id # range_id_1 # range_id_2 # range_1_beg_label_seq_id # range_1_beg_label_atom_id # range_2_beg_label_seq_id # range_2_beg_label_atom_id # range_1_end_label_seq_id # range_1_end_label_atom_id # range_2_end_label_seq_id # range_2_end_label_atom_id A 1_A 2_A 8 O 15 N 8 O 15 N A 2_A 3_A 14 O 58 N 14 O 58 N B 1_B 2_B 18 N 29 O 18 N 29 O B 10_B 11_B 502 O 513 N 502 O 513 N B 2_B 3_B 30 O 99 N 30 O 99 N B 3_B 4_B 100 O 143 N 100 O 143 N B 4_B 5_B 142 O 112 N 142 O 112 N B 5_B 6_B 113 N 195 O 113 N 195 O B 6_B 7_B 196 O 223 N 196 O 223 N B 7_B 8_B 224 O 322 N 224 O 322 N B 8_B 9_B 321 O 421 N 321 O 421 N B 9_B 10_B 420 O 503 N 420 O 503 N loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense #-------#-------#-------#-------#-------#-------#-------#-------#-------#----- #sheet_id # range_id_1 # range_id_2 # offset # sense A 1_A 2_A +1 anti-parallel A 2_A 3_A +1 parallel B 1_B 2_B +1 anti-parallel B 10_B 11_B +1 anti-parallel B 2_B 3_B +1 anti-parallel B 3_B 4_B +1 anti-parallel B 4_B 5_B +1 parallel B 5_B 6_B +1 parallel B 6_B 7_B +1 parallel B 7_B 8_B +1 parallel B 8_B 9_B +1 parallel B 9_B 10_B +1 parallel loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id #-------#-------#-------#-------#-------#-------#-------#-------#-------#----- #sheet_id # id # beg_label_comp_id # beg_label_asym_id # beg_label_seq_id # end_label_comp_id # end_label_asym_id # end_label_seq_id A 1_A LEU * 6 THR * 10 A 2_A GLY * 13 MET * 16 A 3_A VAL * 57 ALA * 60 B 1_B MET * 16 PRO * 21 B 10_B PHE * 502 LEU * 505 B 11_B MET * 510 GLN * 514 B 2_B HIS * 26 PRO * 34 B 3_B TYR * 96 PRO * 102 B 4_B VAL * 142 SER * 147 B 5_B THR * 109 TYR * 116 B 6_B THR * 193 GLU * 199 B 7_B ARG * 220 SER * 226 B 8_B GLN * 318 ASN * 324 B 9_B GLY * 417 PHE * 423
Another example of the need to join and sort multiple tables can be seen in converting reference information to PDB format. The reference information for 4INS [DDH89] in mmCIF format consists of multiple loops with one major concept per loop:
# ----------------------------------------------------------------------------
# CITATION TABLE
loop_
_citation.id
_citation.coordinate_linkage
_citation.title
_citation.country
_citation.journal_abbrev
_citation.journal_volume
_citation.journal_issue
_citation.page_first
_citation.year
_citation.journal_id_ASTM
_citation.journal_id_ISSN
_citation.journal_id_CSD
_citation.book_title
_citation.book_publisher
_citation.book_id_ISBN
_citation.details
#-------#-------#-------#-------#-------#-------#-------#-------#-------#-----
#id #coordinate_linkage
1 no
#title
; The Structure Of 2zn Pig Insulin Crystals At 1.5
Angstroms Resolution
;
#country#journal#volume #issue #page #year
UK
'PHILOS.TRANS.R.SOC.LONDON, SER.B'
319 ? 369 1988
#ASTM #ISSN #CSD
'PTRBAE'
'0080-4622'
441
#book,publisher,ISBN,details
? ? ? ?
#-------#-------#-------#-------#-------#-------#-------#-------#-------#-----
#id #coordinate_linkage
2 no
#title
; A Comparative Assessment Of The Zinc-protein
Coordination In 2Zn-insulin As Determined By X-ray
Absorption Fine Structure (EXAFS) And X-ray
Crystallography
;
#country#journal#volume #issue #page #year
UK 'PROC.R.SOC.LONDON,SER.B'
219 ? 21 1983
#ASTM #ISSN #CSD
'PRLBA4'
'0080-4649'
338
#book,publisher,ISBN,details
? ? ? ?
# [... references 3-14 omitted from this example ...]
#-------#-------#-------#-------#-------#-------#-------#-------#-------#-----
#id #coordinate_linkage
15 no
#title
?
#country#journal#volume #issue #page #year
? ? 5 ? 187 1972
#ASTM #ISSN #CSD
? ? 435
#book,publisher,ISBN,details
; ATLAS OF PROTEIN SEQUENCE
AND STRUCTURE (DATA SECTION)
;
; NATIONAL BIOMEDICAL RESEARCH FOUNDATION,
SILVER SPRING,MD.
;
'0-912466-02-2 ' ?
# ----------------------------------------------------------------------------
# CITATION_EDITOR TABLE
loop_
_citation_editor.citation_id
_citation_editor.name
15 'Dayhoff, M.O.'
# ----------------------------------------------------------------------------
# CITATION_AUTHOR TABLE
loop_
_citation_author.citation_id
_citation_author.name
1 'Baker, E.N.'
1 'Blundell, T.L.'
1 'Cutfield, J.F.'
1 'Cutfield, S.M.'
1 'Dodson, E.J.'
1 'Dodson, G.G.'
1 'Crowfoot Hodgkin, D.M.'
1 'Hubbard, R.E.'
1 'Isaacs, N.W.'
1 'Reynolds, C.D.'
1 'Sakabe, K.'
1 'Sakabe, N.'
1 'Vijayan, N.M.'
2 'Bordas, J.'
2 'Dodson, G.G.'
2 'Grewe, H.'
2 'Koch, M.H.J.'
2 'Krebs, B.'
2 'Randall, J.'
# [... references 3-14 omitted from this example ...]
In PDB format, this information is merged to one block of records per reference:
REMARK 1 REFERENCE 1 REMARK 1 AUTH E.N.Baker,T.L.Blundell,J.F.Cutfield,S.M.Cutfield, REMARK 1 AUTH 2 E.J.Dodson,G.G.Dodson,D.M.Crowfoot Hodgkin, REMARK 1 AUTH 3 R.E.Hubbard,N.W.Isaacs,C.D.Reynolds,K.Sakabe, REMARK 1 AUTH 4 N.Sakabe,N.M.Vijayan REMARK 1 TITL The Structure Of 2zn Pig Insulin Crystals At 1.5 REMARK 1 TITL 2 Angstroms Resolution REMARK 1 REF PHILOS.TRANS.R.SOC.LONDON, V. 319 369 1988 REMARK 1 REFN ASTM PTRBAE UK ISSN 0080-4622 441 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.Bordas,G.G.Dodson,H.Grewe,M.H.J.Koch,B.Krebs, REMARK 1 AUTH 2 J.Randall REMARK 1 TITL A Comparative Assessment Of The Zinc-protein REMARK 1 TITL 2 Coordination In 2Zn-insulin As Determined By X-ray REMARK 1 TITL 3 Absorption Fine Structure (EXAFS) And X-ray REMARK 1 TITL 4 Crystallography REMARK 1 REF PROC.R.SOC.LONDON,SER.B V. 219 21 1983 REMARK 1 REFN ASTM PRLBA4 UK ISSN 0080-4649 338 [... references 3-14 omitted from this example ...] REMARK 1 REFERENCE 15 REMARK 1 EDIT M.O.Dayhoff REMARK 1 REF ATLAS OF PROTEIN SEQUENCE V. 5 187 1972 REMARK 1 REF 2 AND STRUCTURE (DATA SECTION) REMARK 1 PUBL NATIONAL BIOMEDICAL RESEARCH FOUNDATION, SILVER REMARK 1 PUBL 2 SPRING,MD. REMARK 1 REFN ISBN 0-912466-02-2 435
For more examples of mmCIF data and comparisons to PDB format, see the Macromolecular Crystallographic Information (mmCIF) Tutorial [PEB95].
[BB96] is a program which converts mmCIF data sets into "pseudo-PDB" format (a format sufficiently similar to standard PDB format to be accepted by most applications). It is written in Fortran using CIFtbx2 [HB96]. In its present form, it is able to produce HEADER, SCALE, ORIGX, CRYST1, and ATOM/HETATM/TER, which provides sufficient information to drive RASMOL [S94]. It also provides additional record types. The images shown here were produced from CIF's converted to PDB format by cif2pdb and then rendered by RASMOL (a program to do molecular graphics that runs on many platforms).
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)
cif2pdb is used as a filter. If the mmCIF dictionary is stored as a local file name cif_mm.dic, and the program cif2pdb is in your path, then including
... |cif2pdb -d cif_mm.dic -p | ...in a pipeline will convert an mmCIF dataset on the incoming standard input into a pseudo-PDB entry on the outgoing standard output.
There are many useful sites on the World Wide Web where information, tools and software related to CIF, mmCIF and the PDB can be found. The following are good starting points for exploration:
The International Union of Crystallography (IUCr) provides access to software, dictionaries, policy statements and documentation relating to CIF and mmCIF at:
with mirror sites at:The Nucleic Acid Database Project provides access to its entries, software and documentation, with an mmCIF page giving access to the dictionary and mmCIF software tools at:
with mirror sites at:The Protein Data Bank provides access to entries, software and documentation with a browser, and an on-line PDB format description at:
with a mirror sites at:Tutorials on mmCIF and the relationship to PDB format can be found at: http://www.sdsc.edu/pb/cif/tutorials.html
Herbert J. Bernstein (yaya@bernstein-plus-sons.com)