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Translating mmCIF Data into PDB Entries

Based on Translating mmCIF Data into PDB Entries, mmCIF workshop, IUCr meeting, Seattle Washington, August 1996, Abstract E0721

Frances C. Bernstein
Bernstein+Sons, 5 Brewster Lane, Bellport, NY 11713-2803
phone: 1-516-286-1339 email: fcb@bernstein-plus-sons.com

Herbert J. Bernstein
Bernstein+Sons, 5 Brewster Lane, Bellport, NY 11713-2803
phone: 1-516-286-1339 email: yaya@bernstein-plus-sons.com

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)


Introduction


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.

Relationship Between mmCIF and PDB format

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

Syntax


The major differences in syntax are as follows:


mmCIF:

tag-value definitions, little order dependence, strict table structure, upper/lower case, yyyy-mm-dd dates, last-name-first author names, related items may have to appear in disjoint tag-value lists.

PDB:

fixed fields, strongly order dependent, some information non-tabular, upper-case only, dd-mmm-yy dates (dd-mmm-yyyy in some REMARKS), last-name-last author names.

Content

The major differences in content are:

mmCIF:

extensive normalization, works with entities (discrete chemical entities).

PDB:

less normalization, works with chains and HET groups.

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 [BBB98]:

                           
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].

cif2pdb


[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).

Using the Program cif2pdb

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.

4INS

[DDH89] is a PDB entry for Insulin. This image was created by processing 4INS through pdb2cif to produce an mmCIF data set, then through cif2pdb to create a pseudo-PDB entry, and finally through RASMOL.

2ACE

[HRSS96] is a PDB entry for Acetylcholinesterase. This image was created by processing 2ACE through pdb2cif to produce an mmCIF data set, then through cif2pdb to create a pseudo-PDB entry, and finally through RASMOL.

DDF040

[GWB95] is an example mmCIF data set for a DNA-Drug complex structure. It was "born" as an mmCIF data set. This image was created by processing DDF040 through cif2pdb to create a pseudo-PDB entry, and finally through RASMOL.

References

Useful WWW URL's

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: Information and Software for STAR and CIF can be found 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 mirror sites at many locations (see http://www.pdb.bnl.gov/pdb-docs/mirror_sites.html).

Tutorials on mmCIF and the relationship to PDB format can be found at: http://www.sdsc.edu/pb/cif/tutorials.html


Here are direct links to copies of the IUCr CIF home page, the NDB's mmCIF home page, pdb2cif, cif2pdb and CIFtbx (with Cyclops and cif2cif).

United States
NDB, Rutgers, NJ mmCIF pdb2cif cif2pdb CIFtbx...
SDSC, San Diego, CA CIF mmCIF pdb2cif cif2pdb CIFtbx...
United Kingdom
IUCr, Chester CIF   pdb2cif cif2pdb CIFtbx...
EBI, Hinxton   mmCIF pdb2cif cif2pdb CIFtbx...
France
U. P. et M. Curie, Paris CIF pdb2cif cif2pdb CIFtbx...
Sweden
U. of Stockholm CIF   pdb2cif cif2pdb CIFtbx...
South Africa
U. of the Witwatersrand CIF   pdb2cif cif2pdb CIFtbx...
Japan
NIBH, Ibaraki   mmCIF pdb2cif cif2pdb CIFtbx...
Australia
UWA, Nedlands STAR/CIF   pdb2cif cif2pdb CIFtbx...


Updated 24 June 1998

Herbert J. Bernstein (yaya@bernstein-plus-sons.com)