| ## PDBPARSE documentation

## CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES

## 1.0 SUMMARY

Parses PDB files and writes CCF files (clean coordinate files) for proteins

### 1.1 DESCRIPTION

The parsing of protein coordinate data from the Protein Data Bank (PDB) is a common task but is difficult in practice because of an awkward file format, errors in individual PDB files and inconsistencies, particularly in residue numbering. The PDB format is inconvenient for domain-based work or approaches using derived data because PDB files are not annotated with domain definitions and are not easily extended. We required a source of coordinate data that provided fast and convenient access, used an easily parsed, self-consistent format, was specific to proteins, contained minimal bibliographic data, was easily extendible and which could incorporate information on known structural domains as described in SCOP.
We wrote PDBPARSE to parse PDB files reliably and generate 'clean' files of coordinate and derived data, for whole PDB files and, by using the EMBOSS applications SCOPPARSE and DOMAINER, individual structural domains from SCOP. These files fulfil the requirements above and in addition, by using the EMBOSS applications PDBPLUS, can include derived data such as residue solvent accessibility and secondary structure. The files correct several inconsistencies in PDB and employ a consistent residue numbering scheme whilst preserving the numbering from the original PDB file. PDBPARSE identifies over 40 different types of inconsistency, formatting error or other feature of a PDB file that warrant the manual verification of its contents.

## 2.0 INPUTS & OUTPUTS

PDBPARSE parses every PDB file in a directory and writes a protein CCF file (clean coordinate file) for each one. The paths and extensions for the PDB files (input) and protein CCF files (output) files are specified by the user. The user specifies whether the output files have the same names as the input files or whether the PDB identifier codes (from the PDB files) are used to name the files.
The parser generates a log file containing diagnostic messages for various types of inconsistency, error and other features of a PDB file that justify manual inspection of the file to verify its contents (see Section 12.0 below).
PDBPARSE implement the parsing methodology described under 'ALGORITHM' below. The output includes a single file for each PDB file parsed, excluding entries that lack any chains with at least the user-specified minimum number (typically 5) of known amino acids or which lack any SEQRES or ATOM records. The data (described in Section 4.0 and Figure 1) includes the amino acid sequence for each chain (given in the SQ record of a CCF file) and coordinate and derived data for each atom (CO records). Optionally the parser can be configured to mask (disregard) atoms in protein chains as follows: (1) Mask non-amino acid groups that do not contain a C-alpha atom. Masked groups will not appear in either the CO or SQ records. (2) Mask amino acids that do not contain a C-alpha atom. (3) Mask amino acids with a single atom only. For (2) and (3) the residue will not appear in the CO record but will be present in the SQ record.

## 3.0 INPUT FILE FORMAT

An excerpt of a PDB file is shown below (Figure 1). A detailed explanation of the pdb file format is available on the PDB web site: http://www.rcsb.org/pdb/info.html#File_Formats_and_Standards

## 4.0 OUTPUT FILE FORMAT

An excerpt from a protein CCF file is shown below. The data are as follows (record names are given in parentheses):

### 4.1 Bibliographic data

These include the 4-character PDB identifier code or the 7-character domain identifier code taken from SCOP (ID), text from the COMPND (DE) and SOURCE (OS) records of the PDB file and experimental data (EX). Tokens delimiting items of experimental data are as follows. (1) METHOD: The text 'nmr_or_model' for structures determined by nuclear magnetic resonance or modelling, or 'xray' for X-ray crystallography. (2) RESO: The resolution of X-ray structures, or '0' otherwise. (3, 4) NMOD and NCHN: The number of models or polypeptide chains: for domain coordinate files a 1 is always given. (5) NGRP: Number of non-covalently associated groups ('heterogens') that could not be assigned to a specific chain. Spacing lines (XX) are used for improving clarity of the file and the end of file (//) is clearly indicated.

### 4.2 Chain-specific data

Following the EX record the file has a section for each chain, containing the chain number (CN), chain-specific data (IN) and the chain sequence (SQ). Tokens delimiting items of chain-specific data are as follow. (1) ID: The PDB chain identifier or a '.' if one was not specified in the PDB file or if a domain is comprised of segments from more than one chain. (2) NR: The number of residues in the chain or domain. (3) NL: The number of heterogens that are associated with the chain. Domain coordinate files do not include coordinates for these groups so a value of 0 is always given. (4, 5) NH and NE: The number of helices and beta-strands in the chain or domain (see Section 11.2). Values for NH and NE are added by using PDBPLUS and a 0 will be given if PDBPLUS is not used.

### 4.3 Coordinate data

Each CO record contains data for a single atom. The data are in 34 columns in the CO record (column numbers are given in parentheses): (1) CO is always given. (2 - 3) Model and chain number (always 1 for domains). (4) Group number of heterogens or '.'. (5) Either 'P' (a protein atom), 'H' (heterogen) or 'W' (water). (6) Residue number: the position of the residue in the sequence given in the SQ record (for protein atoms) or '.' (for heterogens and water). (7) Original PDB residue number. (8) SSE type from the PDB file: either 'C' (coil), 'H' (helix), 'E' (beta-strand) or 'T' (turn). (9) SSE serial number from columns 8 - 10 in a HELIX, SHEET or TURN record of a PDB file. A '.' is given for atoms not in a helix or sheet. (10) SSE identifier code from columns 12 - 14 in a HELIX, SHEET or TURN record, or '.' for atoms not in a helix or sheet. (11) The class of helix, which is an integer from 1-10; 1 - right-handed alpha, 2 - right-handed omega, 3 - right-handed pi, 4 - right-handed gamma, 5 - right-handed 3-10, 6 - left-handed alpha, 7 - left-handed omega, 8 - left-handed gamma, 9 - 27 ribbon/helix or 10 polyproline; see http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html. (12) Secondary structure assignment according to STRIDE (see Section 11.2). (13) SSE number: the position of the SSE (see Section 11.2) from the N-terminus. A '.' is given if the atom is not in an element. (14) Single character amino acid code or a '.' (for heterogens and water). (15) 3-character residue identifier code. (16) Atom type. (17-19) The x, y and z orthogonal coordinates. (20) Occupancy. (21) Temperature factor. (22-24) Phi and Psi angle and solvent accessible surface area of residue as calculated by STRIDE. (25-34) Accessible surface area according to NACCESS. Absolute and relative measures of accessibility: (25-26) for all atoms, (27-28) all side-chain atoms, (29-30) all main-chain atoms, (31-32) all non-polar side-chain atoms, (33-34) all polar side-chain atoms. Values for records 12-13 and 22-34 are added by using PDBPLUS and a '.' will be given if a value is not available.

### Output files for usage example

### File: pdbparse.log

    /ebi/services/idata/pmr/hgmp/test/data/structure/pdb1cs4.ent
    SEQRESLENDIF   1 (A)
    ATOMCOL12      429
    BADINDEX       1 (A)
    GAPPEDOK       1 (A)
    SECSTART       1 1 ILE 384
    SECSTART       1 1 ILE 384
    //
    /ebi/services/idata/pmr/hgmp/test/data/structure/pdb1ii7.ent
    SEQRESLENDIF   1 (A)
    ATOMCOL12      390
    SECBOTH        1 1 SER 57 GLU 73
    SECBOTH        1 1 VAL 78 ILE 81
    SECBOTH        1 1 LYS 2 LEU 6
    //

### File: 1cs4.ccf

    ID   1cs4
    XX
    DE   MOL_ID: 1; MOLECULE: TYPE V ADENYLATE CYCLASE;
    XX
    OS   MOL_ID: 1; ORGANISM_SCIENTIFIC: CANIS FAMILIARIS;
    XX
    EX   METHOD xray; RESO 2.50; NMOD 1; NCHN 1; NGRP 0;
    XX
    CN   [1]
    XX
    IN   ID A; NR 52; NL 7; NH 0; NE 0;
    XX
    SQ   SEQUENCE    52 AA;   5817 MW;  47362A43 CRC32;
         ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
    XX
    CO   1    1    .    P    2     396   .    .    .    .    .    .    D    ASP    N     51.711  -11.782   62.798    1.00   51.17    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    2     396   .    .    .    .    .    .    D    ASP    CA    52.810  -11.644   61.848    1.00   54.45    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    2     396   .    .    .    .    .    .    D    ASP    C     54.137  -11.314   62.530    1.00   55.11    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    2     396   .    .    .    .    .    .    D    ASP    O     54.175  -10.524   63.469    1.00   55.34    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    2     396   .    .    .    .    .    .    D    ASP    CB    52.437  -10.555   60.831    1.00   57.50    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    2     396   .    .    .    .    .    .    D    ASP    CG    53.460  -10.391   59.729    1.00   61.38    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    2     396   .    .    .    .    .    .    D    ASP    OD1   54.316   -9.485   59.841    1.00   65.55    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    2     396   .    .    .    .    .    .    D    ASP    OD2   53.390  -11.146   58.736    1.00   63.68    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    3     397   .    .    .    .    .    .    I    ILE    N     55.216  -11.941   62.066    1.00   57.14    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    3     397   .    .    .    .    .    .    I    ILE    CA    56.546  -11.705   62.624    1.00   59.46    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    3     397   .    .    .    .    .    .    I    ILE    C     57.020  -10.305   62.230    1.00   60.12    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    3     397   .    .    .    .    .    .    I    ILE    O     56.963   -9.927   61.060    1.00   59.12    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    3     397   .    .    .    .    .    .    I    ILE    CB    57.583  -12.722   62.094    1.00   60.84    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    3     397   .    .    .    .    .    .    I    ILE    CG1   57.184  -14.163   62.447    1.00   63.12    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    3     397   .    .    .    .    .    .    I    ILE    CG2   58.975  -12.384   62.632    1.00   61.24    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    3     397   .    .    .    .    .    .    I    ILE    CD1   57.408  -14.554   63.895    1.00   63.92    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    4     398   .    .    .    .    .    .    E    GLU    N     57.492   -9.548   63.212    1.00   60.23    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    4     398   .    .    .    .    .    .    E    GLU    CA    57.975   -8.198   62.971    1.00   62.14    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    4     398   .    .    .    .    .    .    E    GLU    C     59.401   -8.277   62.424    1.00   60.59    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    4     398   .    .    .    .    .    .    E    GLU    O     60.244   -8.972   62.987    1.00   61.84    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    4     398   .    .    .    .    .    .    E    GLU    CB    57.917   -7.386   64.272    1.00   65.47    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    4     398   .    .    .    .    .    .    E    GLU    CG    58.037   -5.874   64.091    1.00   70.25    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    4     398   .    .    .    .    .    .    E    GLU    CD    57.588   -5.089   65.324    1.00   72.94    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    4     398   .    .    .    .    .    .    E    GLU    OE1   58.262   -5.175   66.377    1.00   70.76    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    4     398   .    .    .    .    .    .    E    GLU    OE2   56.555   -4.380   65.232    1.00   74.36    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    5     399   H    1    1    1    .    .    G    GLY    N     59.642   -7.608   61.298    1.00   57.58    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    5     399   H    1    1    1    .    .    G    GLY    CA    60.956   -7.615   60.681    1.00   56.14    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    5     399   H    1    1    1    .    .    G    GLY    C     61.452   -8.993   60.265    1.00   58.03    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    5     399   H    1    1    1    .    .    G    GLY    O     62.620   -9.322   60.480    1.00   57.47    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    6     400   H    1    1    1    .    .    F    PHE    N     60.576   -9.789   59.649    1.00   58.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    6     400   H    1    1    1    .    .    F    PHE    CA    60.914  -11.143   59.200    1.00   58.07    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    6     400   H    1    1    1    .    .    F    PHE    C     61.995  -11.219   58.117    1.00   58.57    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    6     400   H    1    1    1    .    .    F    PHE    O     62.862  -12.091   58.161    1.00   59.44    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    6     400   H    1    1    1    .    .    F    PHE    CB    59.657  -11.881   58.734    1.00   59.18    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    6     400   H    1    1    1    .    .    F    PHE    CG    59.900  -13.316   58.322    1.00   58.53    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00

      [Part of this file has been deleted for brevity]

    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C9    42.200  -11.309   50.489    1.00   41.39    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    O6    42.275  -12.455   49.593    1.00   43.23    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C10   43.008  -11.601   51.811    1.00   39.11    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C11   40.680  -11.078   50.616    1.00   44.36    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    O7    40.106  -10.945   51.688    1.00   48.77    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C12   39.943  -11.046   49.301    1.00   40.67    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C13   40.595  -10.085   48.292    1.00   41.47    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C14   40.276  -10.620   46.930    1.00   46.69    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C15   39.971  -11.751   46.590    1.00   53.22    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C16   40.047   -8.685   48.426    1.00   42.42    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C17   42.671   -8.737   50.253    1.00   39.67    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C18   46.732  -13.026   51.827    1.00   35.74    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C19   45.859  -11.483   53.586    1.00   34.48    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C20   42.913  -10.426   52.807    1.00   39.44    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C21   45.883   -9.553   47.821    1.00   42.15    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    O5    46.157  -10.520   47.166    1.00   40.91    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     1002  .    .    .    .    .    .    .    FOK    C22   46.769   -8.315   48.006    1.00   37.08    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    O1    45.676    7.326   49.092    1.00   77.86    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    C2    44.367    6.816   48.900    1.00   75.17    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    C3    44.349    5.317   48.923    1.00   74.42    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    N4    44.832    4.804   50.196    1.00   72.45    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    C5    46.234    5.425   50.473    1.00   73.23    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    C6    46.176    6.914   50.355    1.00   75.06    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    C7    44.806    3.336   50.302    1.00   73.39    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    C8    44.672    2.791   51.713    1.00   76.85    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    S     45.724    1.379   51.967    1.00   78.26    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    O1S   47.062    1.828   51.737    1.00   79.39    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    O2S   45.303    0.380   51.016    1.00   81.58    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1003  .    .    .    .    .    .    .    MES    O3S   45.523    0.961   53.326    1.00   80.59    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    O1    59.246   -5.152   27.381    1.00   99.99    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    C2    60.067   -4.021   27.127    1.00   99.99    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    C3    60.447   -3.301   28.378    1.00   99.78    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    N4    61.180   -4.156   29.270    1.00   96.33    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    C5    60.358   -5.461   29.506    1.00   97.90    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    C6    59.965   -6.072   28.203    1.00   99.68    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    C7    61.596   -3.484   30.507    1.00   93.33    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    C8    61.931   -2.010   30.442    1.00   90.74    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    S     60.763   -0.978   31.301    0.50   90.72    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    O1S   59.476   -1.170   30.680    0.50   91.60    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    O2S   61.249    0.383   31.164    0.50   91.20    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     1004  .    .    .    .    .    .    .    MES    O3S   60.776   -1.430   32.647    0.50   90.05    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    7    H    .     1005  .    .    .    .    .    .    .    POP    P1    58.812   -7.766   57.091    1.00   57.40    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    7    H    .     1005  .    .    .    .    .    .    .    POP    O1    60.254   -7.589   56.745    1.00   54.93    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    7    H    .     1005  .    .    .    .    .    .    .    POP    O2    58.618   -8.839   58.095    1.00   55.36    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    7    H    .     1005  .    .    .    .    .    .    .    POP    O3    57.949   -8.024   55.908    1.00   55.10    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    7    H    .     1005  .    .    .    .    .    .    .    POP    O     58.295   -6.370   57.759    1.00   57.30    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    7    H    .     1005  .    .    .    .    .    .    .    POP    P2    56.998   -5.955   58.661    1.00   59.66    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    7    H    .     1005  .    .    .    .    .    .    .    POP    O4    57.491   -5.746   60.070    1.00   54.95    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    7    H    .     1005  .    .    .    .    .    .    .    POP    O5    56.004   -7.075   58.550    1.00   56.24    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    7    H    .     1005  .    .    .    .    .    .    .    POP    O6    56.427   -4.710   58.044    1.00   56.50    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    //

### File: 1ii7.ccf

    ID   1ii7
    XX
    DE   MOL_ID: 1; MOLECULE: MRE11 NUCLEASE;
    XX
    OS   MOL_ID: 1; ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS;
    XX
    EX   METHOD xray; RESO 2.20; NMOD 1; NCHN 1; NGRP 0;
    XX
    CN   [1]
    XX
    IN   ID A; NR 65; NL 6; NH 0; NE 0;
    XX
    SQ   SEQUENCE    65 AA;   7396 MW;  0CFB92A3 CRC32;
         MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
         LKKAI
    XX
    CO   1    1    .    P    8     8     .    .    .    .    .    .    D    ASP    N      7.977   32.254   19.055    1.00   26.65    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    8     8     .    .    .    .    .    .    D    ASP    CA     8.882   31.149   19.290    1.00   28.34    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    8     8     .    .    .    .    .    .    D    ASP    C     10.273   31.305   18.659    1.00   27.71    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    8     8     .    .    .    .    .    .    D    ASP    O     10.740   30.453   17.907    1.00   29.27    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    8     8     .    .    .    .    .    .    D    ASP    CB     8.186   29.886   18.777    1.00   30.25    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    8     8     .    .    .    .    .    .    D    ASP    CG     6.918   29.584   19.554    1.00   34.25    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    8     8     .    .    .    .    .    .    D    ASP    OD1    7.041   29.177   20.724    1.00   33.37    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    8     8     .    .    .    .    .    .    D    ASP    OD2    5.801   29.770   19.010    1.00   35.77    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    9     9     .    .    .    .    .    .    I    ILE    N     10.913   32.423   18.967    1.00   26.84    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    9     9     .    .    .    .    .    .    I    ILE    CA    12.236   32.739   18.477    1.00   26.52    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    9     9     .    .    .    .    .    .    I    ILE    C     13.285   31.864   19.173    1.00   28.22    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    9     9     .    .    .    .    .    .    I    ILE    O     14.257   31.426   18.550    1.00   28.01    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    9     9     .    .    .    .    .    .    I    ILE    CB    12.520   34.214   18.759    1.00   27.25    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    9     9     .    .    .    .    .    .    I    ILE    CG1   11.338   35.051   18.249    1.00   26.35    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    9     9     .    .    .    .    .    .    I    ILE    CG2   13.823   34.640   18.094    1.00   26.40    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    9     9     .    .    .    .    .    .    I    ILE    CD1   11.011   34.845   16.725    1.00   25.85    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    N     13.072   31.599   20.462    1.00   26.69    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    CA    14.009   30.787   21.254    1.00   28.02    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    C     15.483   31.203   21.181    1.00   27.57    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    O     16.357   30.359   21.019    1.00   23.99    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    CB    13.867   29.284   20.899    1.00   27.15    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    CG    12.599   28.681   21.415    1.00   28.59    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    ND1   12.536   27.980   22.603    1.00   30.06    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    CD2   11.319   28.794   20.978    1.00   26.35    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    CE1   11.276   27.691   22.875    1.00   27.36    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    10    10    .    .    .    .    .    .    H    HIS    NE2   10.519   28.180   21.909    1.00   28.44    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    11    11    .    .    .    .    .    .    L    LEU    N     15.758   32.503   21.303    1.00   26.85    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    11    11    .    .    .    .    .    .    L    LEU    CA    17.152   32.972   21.286    1.00   27.57    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    11    11    .    .    .    .    .    .    L    LEU    C     17.879   32.257   22.409    1.00   28.11    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    11    11    .    .    .    .    .    .    L    LEU    O     17.323   32.093   23.505    1.00   29.47    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    11    11    .    .    .    .    .    .    L    LEU    CB    17.225   34.494   21.530    1.00   25.89    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    11    11    .    .    .    .    .    .    L    LEU    CG    16.526   35.348   20.465    1.00   23.73    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    11    11    .    .    .    .    .    .    L    LEU    CD1   16.604   36.805   20.823    1.00   24.72    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    11    11    .    .    .    .    .    .    L    LEU    CD2   17.179   35.102   19.081    1.00   22.96    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00

      [Part of this file has been deleted for brevity]

    CO   1    1    .    P    50    50    .    .    .    .    .    .    L    LEU    CD2   12.425   39.035   22.798    1.00   23.77    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    1    H    .     402   .    .    .    .    .    .    .    PO4    P     34.178   32.996   46.387    1.00   60.84    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    1    H    .     402   .    .    .    .    .    .    .    PO4    O1    35.146   33.243   45.291    1.00   57.95    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    1    H    .     402   .    .    .    .    .    .    .    PO4    O2    34.912   32.751   47.670    1.00   59.15    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    1    H    .     402   .    .    .    .    .    .    .    PO4    O3    33.291   34.184   46.538    1.00   58.92    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    1    H    .     402   .    .    .    .    .    .    .    PO4    O4    33.352   31.796   46.060    1.00   61.86    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    2    H    .     403   .    .    .    .    .    .    .     MN    MN     8.130   27.788   21.899    1.00   36.09    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    2    H    .     404   .    .    .    .    .    .    .     MN    MN     5.801   27.935   24.271    1.00   39.57    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    3    H    .     405   .    .    .    .    .    .    .     MN    MN    36.023   34.916   44.253    1.00   39.52    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    3    H    .     406   .    .    .    .    .    .    .     MN    MN    33.658   36.365   46.296    1.00   33.69    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     501   .    .    .    .    .    .    .    SO4    S     17.175   28.112   32.476    1.00  100.80    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     501   .    .    .    .    .    .    .    SO4    O1    18.136   28.230   31.357    1.00  100.18    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     501   .    .    .    .    .    .    .    SO4    O2    17.097   26.692   32.887    1.00  100.80    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     501   .    .    .    .    .    .    .    SO4    O3    17.633   28.926   33.626    1.00  100.14    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     501   .    .    .    .    .    .    .    SO4    O4    15.834   28.575   32.045    1.00  100.56    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     502   .    .    .    .    .    .    .    SO4    S      0.566   29.512   36.007    1.00   86.73    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     502   .    .    .    .    .    .    .    SO4    O1     1.690   28.556   35.971    1.00   87.27    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     502   .    .    .    .    .    .    .    SO4    O2    -0.620   28.803   36.523    1.00   87.87    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     502   .    .    .    .    .    .    .    SO4    O3     0.896   30.642   36.905    1.00   86.58    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     502   .    .    .    .    .    .    .    SO4    O4     0.287   30.037   34.658    1.00   86.51    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     503   .    .    .    .    .    .    .    SO4    S    -13.586   39.644   36.031    1.00  100.28    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     503   .    .    .    .    .    .    .    SO4    O1   -12.340   39.512   35.250    1.00  100.72    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     503   .    .    .    .    .    .    .    SO4    O2   -14.638   38.811   35.421    1.00  100.46    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     503   .    .    .    .    .    .    .    SO4    O3   -13.347   39.201   37.420    1.00   99.66    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    5    H    .     503   .    .    .    .    .    .    .    SO4    O4   -14.020   41.056   36.015    1.00   99.97    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    P      7.599   25.305   23.994    1.00   56.33    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    O1P    8.249   24.467   25.030    1.00   56.70    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    O2P    6.700   26.285   24.649    1.00   54.49    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    O3P    8.637   26.026   23.216    1.00   53.97    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    O5*    7.095   23.970   23.128    1.00   59.20    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C5*    7.073   23.961   21.762    1.00   66.74    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C4*    6.041   23.013   21.296    1.00   71.22    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    O4*    6.029   21.855   22.189    1.00   73.78    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C3*    4.736   23.676   21.350    1.00   73.80    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    O3*    4.355   23.874   19.995    1.00   76.51    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C2*    3.864   22.749   22.165    1.00   74.04    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C1*    4.682   21.474   22.506    1.00   74.70    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    N9     4.578   21.123   23.969    1.00   76.71    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C8     3.630   21.533   24.876    1.00   76.87    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    N7     3.758   21.069   26.081    1.00   77.50    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C5     4.896   20.300   25.989    1.00   77.78    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C6     5.570   19.479   26.941    1.00   78.16    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    N6     5.155   19.409   28.200    1.00   78.77    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    N1     6.682   18.805   26.554    1.00   78.32    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C2     7.090   18.888   25.277    1.00   78.14    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    N3     6.541   19.611   24.271    1.00   78.05    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    6    H    .     401   .    .    .    .    .    .    .    101    C4     5.403   20.288   24.700    1.00   78.10    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     407   .    .    .    .    .    .    .    HOH    O      5.997   27.242   22.189    1.00   38.84    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     408   .    .    .    .    .    .    .    HOH    O     35.697   35.756   46.350    1.00   41.39    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     600   .    .    .    .    .    .    .    HOH    O     20.825   31.690   27.031    1.00   20.90    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    //

## 5.0 DATA FILES

PDBPARSE does not use a data file.

## 6.0 USAGE

### 6.1 COMMAND LINE ARGUMENTS

       Standard (Mandatory) qualifiers:
      [-pdbpath]           dirlist    This option specifies the location of PDB
                                      files (input). A PDB file contains protein
                                      coordinate and other data. A detailed
                                      explanation of the PDB file format is
                                      available on the PDB web site
                                      http://www.rcsb.org/pdb/info.html.
       -camask             boolean    This option specifies whether to to mask
                                      non-amino acid groups in protein chains that
                                      do not contain a C-alpha atom. If masked,
                                      the group will not appear in either the CO
                                      or SQ records of the clean coordinate file.
       -camaska            boolean    This option specifies whether to mask amino
                                      acids in protein chains that do not contain
                                      a C-alpha atom. If masked, the amino acid
                                      will not appear in the CO record but will
                                      still be present in the SQ record of the
                                      clean coordinate file.
       -atommask           boolean    This option specifies whether to mask amino
                                      acid residues in protein chains with a
                                      single atom only. If masked, the amino acid
                                      will appear not appear in the CO record but
                                      will still be present in the SQ record of
                                      the clean coordinate file.
      [-ccfoutdir]         outdir     This option specifies the location of CCF
                                      files (clean coordinate files) (output). A
                                      'protein clean cordinate file' contains
                                      protein coordinate and other data for a
                                      single PDB file. The files, generated by
                                      using PDBPARSE, are in CCF format
                                      (EMBL-like) and contain 'cleaned-up' data
                                      that is self-consistent and error-corrected.
                                      Records for residue solvent accessibility
                                      and secondary structure are added to the
                                      file by using PDBPLUS.
       -errfile            outfile    This option specifies tame of the log file
                                      for the build. The log file may contain
                                      messages about inconsistencies or errors in
                                      the PDB files that were parsed.

       Additional (Optional) qualifiers:
       -[no]ccfnaming      boolean    This option specifies whether to use pdbid
                                      code to name the output files. If set, the
                                      PDB identifier code (from the PDB file) is
                                      used to name the file. Otherwise, the output
                                      files have the same names as the input
                                      files.
       -chnsiz             integer    Minimum number of amino acid residues in a
                                      chain for it to be parsed.
       -maxmis             integer    Maximum number of permissible mismatches
                                      between the ATOM and SEQRES sequences.
       -maxtrim            integer    Max. no. residues to trim when checking for
                                      missing C-terminal SEQRES sequences.

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-errfile" associated qualifiers
       -odirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write standard output
       -filter             boolean    Read standard input, write standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report deaths

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-pdbpath] (Parameter 1) | This option specifies the location of PDB files (input). A PDB file contains protein coordinate and other data. A detailed explanation of the PDB file format is available on the PDB web site http://www.rcsb.org/pdb/info.html. | Directory with files | ./
-camask | This option specifies whether to to mask non-amino acid groups in protein chains that do not contain a C-alpha atom. If masked, the group will not appear in either the CO or SQ records of the clean coordinate file. | Boolean value Yes/No | No
-camaska | This option specifies whether to mask amino acids in protein chains that do not contain a C-alpha atom. If masked, the amino acid will not appear in the CO record but will still be present in the SQ record of the clean coordinate file. | Boolean value Yes/No | No
-atommask | This option specifies whether to mask amino acid residues in protein chains with a single atom only. If masked, the amino acid will appear not appear in the CO record but will still be present in the SQ record of the clean coordinate file. | Boolean value Yes/No | No
[-ccfoutdir] (Parameter 2) | This option specifies the location of CCF files (clean coordinate files) (output). A 'protein clean cordinate file' contains protein coordinate and other data for a single PDB file. The files, generated by using PDBPARSE, are in CCF format (EMBL-like) and contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. | Output directory | ./
-errfile | This option specifies tame of the log file for the build. The log file may contain messages about inconsistencies or errors in the PDB files that were parsed. | Output file | pdbparse.log
Additional (Optional) qualifiers | Allowed values | Default
-[no]ccfnaming | This option specifies whether to use pdbid code to name the output files. If set, the PDB identifier code (from the PDB file) is used to name the file. Otherwise, the output files have the same names as the input files. | Boolean value Yes/No | Yes
-chnsiz | Minimum number of amino acid residues in a chain for it to be parsed. | Any integer value | 5
-maxmis | Maximum number of permissible mismatches between the ATOM and SEQRES sequences. | Any integer value | 3
-maxtrim | Max. no. residues to trim when checking for missing C-terminal SEQRES sequences. | Any integer value | 10
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

### 6.2 EXAMPLE SESSION

An example of interactive use of PDBPARSE is shown below. Here is a sample session with pdbparse

    % pdbparse
    Parses PDB files and writes CCF files (clean coordinate files) for
    proteins.
    Location of PDB files (input) [./]: structure
    Mask non-amino acid groups in protein chains that do not contain a C-alpha atom. [N]:
    Mask amino acids in protein chains that do not contain a C-alpha atom. [N]: Y
    Mask amino acid residues in protein chains with a single atom only. [N]:
    Location of CCF files (clean coordinate files) (output) [./]:
    Name of log file for the build. [pdbparse.log]:

    Processing /ebi/services/idata/pmr/hgmp/test/data/structure/pdb1cs4.ent
    Processing /ebi/services/idata/pmr/hgmp/test/data/structure/pdb1ii7.ent

Go to the output files for this example

The PDB files pdb1ii7.ent and pdb1cs4.ent were read. The protein clean coordinate files 1cs4.ccf and 1ii7.ccf are written. A log file called /test_data/pdbparse/pdbparse.log was also written.

## 7.0 KNOWN BUGS & WARNINGS

Although our parsing methodology was validated by the manual comparison of many "clean" files to their respective PDB files, it was clearly not possible to check every file. Any errors should be reported to the authors.
PDBPARSE is not guaranteed to work correctly (or even at all) for files where an NMR structure contains multiple models but the models have different sequence of residues due to errors.
PDBPARSE will not work in cases where a residue number is duplicated AND an alternative residue numbering system is used somewhere else in the same chain. If such cases exist they could be parsed by having a variable corresponding to oddnum (see pdbparse.c), but just for duplicate residue positions. The new variable would get written in the same place as oddnum is written.
The author does not know whether either of the above cases occur in pdb.
PDBPARSE necessarily must hold the entire PDB file and some derived data in memory. If an error of the type 'Uncaught exception: Allocation failed, insufficient memory available' is raised then this is probably because the memory requirements exceed per-user memory defaults (that are usually set quite low). This can easily be unlimited in the login process. If tcsh is used, then simply type 'unlimit' before PDBPARSE is run.

## 8.0 NOTES

Clean coordinate files are available from
ftp://ftp.uk.embnet.org/pub/databases/structure/cleancoord.
A list of problematic features in individual PDB files is available at
ftp://ftp.uk.embnet.org/pub/databases/structure/cleancoord/pdbparse.log.
Values in the CCF file for the number of helices (NH) or beta-strands (NE) in a chain and columns 12-13 and 22-34 of the coordinate line record (CO) are given null values ('.' or 0) by PDBPARSE (see Section 4.0). The EMBOSS program PDBPLUS can be used to assign values to these these records.

### 8.1 GLOSSARY OF FILE TYPES

FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO
Clean coordinate file (for protein) | CCF format (EMBL-like format for protein coordinate and derived data). | Coordinate and other data for a single PDB file. The data are 'cleaned-up': self-consistent and error-corrected. | PDBPARSE | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.

None

## 9.0 DESCRIPTION

The Protein Data Bank [1, 2] was established some 30 years ago at the Brookhaven National Laboratories as a repository for protein X-ray crystallographic data. The original design used an ASCII file format based on punched cards. Today, PDB uses a relational database management system and is managed by the Research Collaboratory for Structural Bioinformatics (RCSB) in collaboration with the European Macromolecular Structure Database (EMSD). Query tools such as the web-based PDBbrowse [3], SearchFields (http://www.rcsb.org/pdb/queryForm.cgi), MSDLite (http://www.ebi.ac.uk/msd-srv/msdliindex.html) and MSDPro (http://www.ebi.ac.uk/msd-srv/msdpindex.html) are useful for the analysis of a single or a few protein structures, but are an inconvenient source of coordinate data and are inappropriate for global, automated analyses. A researcher commonly needs direct access to the coordinate data, however the text files provided are notoriously difficult to parse reliably. The problems arise from errors in individual PDB files and an awkward and inconsistent file format, which has evolved in a seemingly ad hoc manner to cope with increasing amounts of bibliographic and macromolecular coordinate data from a variety of experimental techniques. Difficulties in parsing can only compound problems arising from anomalies with the coordinate data themselves: over a million "outliers" in PDB have been identified [4], reflecting discrepancies with conventions, statistical outliers and probable errors.
A particularly difficult aspect of parsing is determining the sequence of residues and ensuring that the atomic coordinates are assigned to the correct sequence position in the relevant data structure. The biological amino acid sequence (given in the SEQRES records of a PDB file) frequently differs from the sequence of residues (given in the ATOM records) for which coordinates are available. PDB does not consistently use a sequential residue numbering scheme and residue numbers must be treated as strings. Although a mapping between the ATOM and SEQRES records can be obtained automatically by using the pdb2cif program [5], these contain errors owing to mistakes and inconsistencies in PDB. The authors of the ASTRAL compendium [6] identified some of the types of error and provide manual corrections to the pdb2cif mappings in their Rapid Access Format (RAF) database [7].
Although extensive validation is now performed on deposited data, including comparisons of PDB SEQRES and ATOM records, there is a legacy of PDB files that predate these quality control measures. Extensive efforts are being made by the RCSB and the EMSD to clean up the legacy files. For example, database constrains are used by MSD to maintain data integrity in their archive database so that inconsistencies (primarily in bibliographic, chemical and coordinate data) do not appear in the search database. Further difficulties in processing PDB data arise in cases unrelated to file formatting, for example where multiple sets of coordinates are given for an individual atom or whole residue, where coordinates for only a single atom of a residue are given, where C-alpha atoms are missing or where coordinates for non-amino acid groups are given in polypeptide chains. Further, if a method uses protein domains such as those described in the SCOP database [8], coordinates for the domain have to be extracted from the PDB file. Fortunately, the SCOP domain definitions use the original PDB residue numbers taken from the ATOM records. Nonetheless, this presents an extra layer of complexity in parsing the data. For example, a SCOP domain may span more than one PDB chain or be composed of fragments from the same or different chains.
We required a source of coordinate data that provided fast and convenient access, used an easily parsed, self-consistent format, was specific to proteins, contained minimal bibliographic data, correctly employed a consistent residue numbering scheme whilst preserving the original numbering, was easily extendible and which incorporated information on known structural domains as described in SCOP. We have written software to parse PDB files reliably and generate "cleaned up" flat text files of protein coordinate and derived data, for whole PDB files and individual SCOP domains. These files fulfil the requirements above and in addition include derived data such as residue solvent accessibility and secondary structure. Flexible masking of coordinate data for problematic residues, for example those lacking coordinates for a C-alpha atom, is also provided by the software. our software, the parsing methodology, the content and format of our CCF files. This work complements other groups who have worked towards handling the PDB data, for example [9].
The parsing of PDB files is highly inconvenient, time-consuming and potentially a major source of error in important fields such as molecular modelling, drug design, protein docking experiments, protein folding studies, protein structure comparison and threading. In fact, problems manifest in any method that uses PDB data and relies on an acurate mapping of the biological sequence to the available coordinates. Only a single error, for example in assigning coordinate or derived data to the correct position in a data structure, may be required to poison an entire analysis. Further, different interpretations of the PDB files by different groups might lead to inconsistencies between these analyses. PDBPARSE is used to generate files of coordinate data for protein chains and domains in an easily parsed, self-consistent format in which many inconsistencies and problematic features of the original PDB files, particularly in residue numbering, have been corrected. The original residue numbers are preserved, however, so that it's unnecessary to learn a new set of residue numbering conventions and comparisons to the original files and to the approaches of other groups is easy. The files can be annotated with useful derived data, for example, by using the PDBPLUS application. This further increases their usefulness.
Options to mask data for problematic residues and the capacity to generate derived data from the coordinates for whole proteins or individual domains add further flexibility to our software. The fast and reliable parsing of CCF files is a trivial matter: appropriate software is available in EMBOSS as part of the AJAX C programming library. We hope CCF files will be useful, for example, in the construction of secondary databases.

## 10.0 ALGORITHM

Some of the tasks and difficulties involved in parsing a PDB file are summarized below. The numbered tasks refer to the 'Methodology for parsing PDB files' described in the text.

### 10.1 Summary of difficulties in parsing a PDB file

### 10.1.1 Count models.

The number of models is normally equal to the number of MODEL records, but NMR structures with only a single model sometimes lack a MODEL record.

### 10.1.2. Count chains and assign chain identifier, sequence and length (residues).

SEQRES records do not consistently include heterogens, or non-amino acid groups in polypeptide chains. The type of molecule (protein, nucleic acid or polysaccharide) is not clearly indicated. The indicated and actual number of SEQRES residues can differ. Rarely, chains are given in the SEQRES records but are missing from the ATOM records.

### 10.1.3. Parse coordinates for individual chains.

Some files do not contain any TER records or have multiple chains that are not delimited by TER records. Multiple TER records are given for a single chain where the coordinates are for fragments of a protein digest. Occasionally, the TER record does not delimit the protein and heterogen atoms, but is given after the final heterogen atom instead. The order of chains in the SEQRES records may not agree with that in the ATOM records. Errors may occur in the use of chain identifiers, especially for N and C-terminal residues.

### 10.1.4. Parse coordinates for non-covalently associated groups (heterogens) and assign them to chains.

Chain identifiers are not consistently used and might differ from that of the chain to which the group is associated. Occasionally all the heterogen atoms are listed together after the last chain in the structure rather being than associated with individual chains.

### 10.1.5. Identify heterogeneous residue positions.

Residue numbering for heterogeneous positions is not handled consistently. For example, both insertion codes and non-sequential numbers are used.

### 10.1.6. Process non-sequential and character-based numbering systems

Coordinates might be given for a fragment and residue numbering is relative to the full length protein. Residue numbering might be relative to a sequence or topological alignment. For example, insertion codes (characters) are used in cases where numbering is given relative to a reference protein and the homologue possesses certain residues that the reference protein lacks. Insertion codes might also be used to indicate insertion mutations.

### 10.1.7. Process jumps in residue numbering.

Jumps in residue numbering may arise systematically, for example where parts of the structure could not be refined or where residue numbering is given relative to a reference protein and the homologue lacks certain residue(s) in the reference protein. Other jumps are the result of errors.

### 10.1.8. Process residue numbering at the N-terminus.

N-terminal MET residues and blocking groups are often numbered zero (rather than 1) but this also occurs for other N-terminal residues. In some files, for reasons of alignment, the N-terminal residue is assigned a negative number and the residue C-terminal to residue -1 can be numbered +1 or 0. Sometimes the indicated starting residue number is either higher or lower than suggested by the SEQRES records.

### 10.2 Parsing methodology

The following text is numbered to correspond to the text above. The PDB file is read into memory and the number of models (sets of coordinates) is determined (1). The SEQRES records are parsed to determine the number of unique polypeptide chains and the chain identifier, amino acid sequence ('SEQRES sequence') and length (residues) of each chain (2). Coordinates for individual chains and heterogens are parsed for every model. Coordinates for a chain are normally indicated by the presence of an ATOM or HETATM record before a TER record and containing the relevant chain identifier, with the coordinates for heterogens appearing after the TER record. There are, however, many inconsistencies (3 and 4) that the parser manages. Each heterogen is assigned to a chain where possible and given a group number relative to either the chain with which is associated or the whole protein. Thus a heterogen is uniquely identified by its chain number (if available) and group number. Where multiple coordinates are given for a single atom or residue the first set of coordinates are used and the others discarded. Such cases are distinguished from residue heterogeneity (5), which may arise naturally or if a residue has been partly chemically modified. There are many difficulties in assigning the correct residue sequence and numbering for a chain. Non-sequential and character-based numbering systems are used (6), producing many examples where the residue numbering in the ATOM records does not agree at all with the SEQRES records. Jumps in residue numbering occur (7), and incorrect residue identifiers result in mismatches between the ATOM and SEQRES records. N-terminal MET residues and blocking groups listed in the ATOM records are frequently missing from the SEQRES records and there are serious inconsistencies in residue numbering at the N-terminus (8). Other N and C-terminal residues are occasionally omitted from the SEQRES records. The correct residue sequence and numbering for a chain is determined by an alignment of the 'SEQRES sequence' and an 'ATOM sequence' that is extracted from the ATOM records of the PDB file. The alignment procedure is summarised in Figure 3 and described in 6 steps below.

### 10.2.1. (Step 1) Mark up ambiguous positions

- The character position used in PDB files to indicate heterogeneity is also used in the character-based numbering schemes. Such ambiguous residue positions are recorded.

### 10.2.2. (Step 2) Check residue numbering (presuming a character-based numbering system)

- Each residue in the ATOM sequence is assigned a positive and incremental residue number based on the original PDB residue number; non-sequential or character-based numbering schemes are replaced. However, any jumps in the residue numbering are preserved. A copy of the original PDB residue numbering is also preserved. The SEQRES sequence is corrected for any missing N- or C-terminal groups. At this stage, ATOM records are presumed to use a character-based numbering scheme rather than contain heterogeneity and no errors (residue mismatches between the ATOM and SEQRES sequences) are allowed. If the ATOM sequence is a sub-string of the SEQRES sequence or the residue numbering agrees with the SEQRES sequence, the SEQRES sequence is taken as the biological sequence, residue numbers for the chain are assigned and no further steps are necessary.

### 10.2.3. (Step 3) Align ATOM and SEQRES sequences (presuming a character-based numbering system)

- An alignment of the ATOM and SEQRES sequences is sought by identifying exact string matches between sub-strings of the ATOM sequence and the full-length SEQRES sequence. Consider the alignment of an ATOM sequence (A) of 100 residues (A1, A2 A100) to a SEQRES sequence of 120 residues (S1, S2 S120). First, the parser checks for an exact match of A to S, and if none is found sub-strings of A of progressively smaller size are tested; A1-A99 first, then A1-A98 and so on until an exact match is found or an exact match for a single residue only (A1) cannot be found. A sub-string of A can be matched to any region in the SEQRES sequence, but exact matches are discarded if they would not leave sufficient space in the SEQRES sequence (C-terminal to the matched region) for the alignment of the remainder of the ATOM sequence.
Imagine an example where A1-A50 matches exactly S11-S60, but A51 does not match S61. To continue the alignment, the parser searches for an exact match for the remainder of the ATOM sequence, A51-A100, then A51-A99, A51-58 as before. The sub-string can be matched to any region in the SEQRES sequence beginning from position 61 onwards, so long as it would leave space for the remainder of the ATOM sequence as before. Gaps between successive matching regions are allowed and in this manner SEQRES residues missing from the ATOM records are detected and residue numbers assigned. If, for example, A51-A100 matched exactly S62 S111, then the ATOM sequence is missing a single residue (SEQRES residue 61) relative to the SEQRES sequence.

### 10.2.4. (Step 4) Check alignment (presuming heterogeneity)

- If, after string alignment, an exact match is not found for all positions in the ATOM sequence, steps 2. and 3. are repeated but heterogeneity is presumed rather than an alternative numbering scheme; redundant sets of coordinates for heterogeneous positions are masked from the ATOM sequence.

### 10.2.5. (Step 5) Check alignment (allowing mismatches)

- If an exact match still cannot be found for all positions in the ATOM sequence, steps 2 - 4. are repeated, but this time a user-defined number (typically 3) of mismatches between the SEQRES and ATOM positions are allowed. The "true" residue (i.e. the one that will be given in the protein sequence in the output file) is that from the ATOM records. For example, in cases where the lengths of the two sequences are the same but the sequences differ, the sequence from the ATOM records is taken to be the true sequence.

### 10.2.6. (Step 6) Default assignment

- If, after step 5., the ATOM and SEQRES sequences could not be matched (allowing up to the maximum number of mismatches), the raw ATOM sequence is taken to be the true sequence in which case the assignment of residue numbers is trivial. Thus the alignment procedure uses the following priority when finding the correct alignment of the ATOM and SEQRES sequences: (1) No gap insertion or mismatches required. (2) Gap insertion with no mismatches. (3) Mismatches but no gaps. (4) Gap insertion and mismatches. (5) Default of raw ATOM sequence is used and SEQRES sequence is discarded.
Figure 3 Schematic diagram of alignment procedure

## 11.0 RELATED APPLICATIONS

## See also

Program name | Description
--- | ---
aaindexextract | Extract data from AAINDEX
allversusall | Does an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values
cathparse | Reads raw CATH classification files and writes DCF file (domain classification file)
cutgextract | Extract data from CUTG
domainer | Reads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file)
domainnr | Removes redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS
domainseqs | Adds sequence records to a DCF file (domain classification file)
domainsse | Adds secondary structure records to a DCF file (domain classification file)
hetparse | Converts raw dictionary of heterogen groups to a file in EMBL-like format
pdbplus | Add residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain
pdbtosp | Convert raw swissprot:PDB equivalence file to EMBL-like format
printsextract | Extract data from PRINTS
prosextract | Builds the PROSITE motif database for patmatmotifs to search
rebaseextract | Extract data from REBASE
scopparse | Reads raw SCOP classification files and writes a DCF file (domain classification file)
seqnr | Removes redundancy from DHF files (domain hits files) or other files of sequences
sites | Reads CCF files (clean coordinate files) and writes CON files (contact files) of residue-ligand contact data for domains in a DCF file (domain classification file)
ssematch | Searches a DCF file (domain classification file) for secondary structure matches
tfextract | Extract data from TRANSFAC

### 11.1 Domain coordinate data

We wrote the DOMAINER application to read protein CCF files and generate files of coordinates for single SCOP domains in the CCF format (domain CCF files, Figure 1) and the PDB format. DOMAINER reads a file of SCOP classification data that is prepared by using the application SCOPPARSE, and generates an output file in each format for each domain listed. Where coordinates for multiple models were determined, data in the output files are given for the first model only. In cases where a domain consists of sections from more than one polypeptide chain, the data are presented as belonging to a single chain only (a single sequence with a chain identifier of is given). SCOPPARSE was written to parse the raw SCOP classification files (dir.cla.scop.txt and dir.des.scop.txt) available at URL (http://scop.mrc-lmb.cam.ac.uk/scop/parse/) and generate an output file suitable for use with DOMAINER.

### 11.2 Derived data

We wrote the PDBPLUS application, as a wrapper to the STRIDE [10] and NACCESS [11] programs, to add the derived data (i - iv below) to a CCF file. PDBPLUS runs on both protein and domain CCF files and requires corresponding files in PDB format, either the original PDB file (for proteins) or one generated by using DOMAINER (for domains). The values of the derived data for a given residue will of course depend on whether they were calculated from the coordinates for the entire structure or just the domain. Thus PDBPLUS provides useful flexibility in generating the derived data.
i. Absolute (Abs.) and relative (Rel.) accessible surface area of residues according to NACCESS. Abs. is the summed accessible surface area of the atoms, whereas Rel. is expressed as a percentage relative to the accessibility of the atoms in an extended ALA-x-ALA tri-peptide conformation. The NACCESS authors treat alpha carbons as side-chain atoms so that glycine can have a value for side-chain accessible surface area (see 'Database format' below). They are therefore not included in the main-chain.
ii. Phi and Psi angle and solvent accessible surface area of residues as calculated by using STRIDE.
iii. Secondary structure assignment according to STRIDE, one of 'H' (alpha helix), 'G' (3-10 helix), 'I' (Pi-helix), 'E' (extended conformation), 'B' or 'b' (isolated bridge), 'T' (turn) or 'C' (coil, i.e. none of the above).
iv. The number of helical or beta-strand secondary structure elements (SSEs) in the chain or domain. An 'element' is defined as a run of a user-defined number (typically 4) of residues in the 'H', 'G' or 'I' conformation (helices) or the 'E' conformation (beta-strands).

## 12.0 DIAGNOSTIC ERROR MESSAGES

### 12.1 Features of a PDB file diagnosed during parsing

Listed below are various types of inconsistencies, errors or other dubious features of a PDB file identified by PDBPARSE. The first line of each block are examples of diagnostic messages that may appear in the log file generated by PDBPARSE. The second line is a description / action taken and the third line is the number of times the error message is reported, e.g. "Chain" means the error is reported for each chain as appopriate.

    FILE_OPEN      my.file
    my.file could not be opened for reading or writing.  The file is ignored.
    File

    FILE_READ      my.file
    my.file could not be read.  The file is ignored.
    File

    NO_OUTPUT      my.file
    No clean coordinate file was generated for my.file.  This will happen if there was a FILE_READ error on the raw PDB file, or a NOSEQRES, NOATOM or NOPROTEINS error when reading the file.
    File

    FILE_WRITE     my.file
    my.file could not be written. The file is ignored.
    File.

    BADINDEX 1 (A)
    Raw residue numbering from ATOM records does not give the correct index into the SEQRES sequence for chain 1 ('A'). The correct alignment of the ATOM and SEQRES sequences is found by string handling (see 'Parsing methodology' in the text).
    Chain

    NEGNUM 1 (A) 123
    Negative residue number found for chain 1 ('A') on line 123.
    Chain

    ZERNUM 1 (A) 123
    Residue number of zero found for chain 1 ('A') on line 123.
    Chain

    ODDNUM 1 (A) 123
    Possible residue heterogeneity or alternative residue numbering scheme for chain 1 ('A') on line 123.
    Chain

    NONSQNTL 1 (A) 123
    Possible case of non-sequential numbering error for chain 1 ('A') on line 123.
    Chain

    HETEROK 1 (A)
    Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found by presuming an alternative residue numbering scheme.
    Chain

    ALTERNOK 1 (A)
    Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found by presuming one or more instances of heterogeneity.
    Chain

    MISSNTERM 1 (A) 3
    SEQRES records appeared to be missing 3 N-terminal residues relative to ATOM sequence for chain 1 ('A'). The missing residues are added to the sequence.
    Chain

    MISSCTERM 1 (A) 3
    SEQRES records appeared to be missing 3 C-terminal residues relative to ATOM sequence for chain 1 ('A'). The missing residues are added to the sequence.
    Chain

    GAPPEDOK 1 (A)
    Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found by gap insertion with no mismatches.
    Chain

    MISMATCH 1 (A) 2 ALA 2 ARG 6;    ALA 12 TYR 16
    Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found without gap insertion but contained 2 mismatches (ALA 2 versus ARG 6 and ALA 12 versus TYR 16).
    Chain

    GAPPED 1 (A) 2 ALA 2 ARG 6;    ALA 12 TYR 16
    Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') found by gap insertion but contained 2 mismatches (ALA 2 versus ARG 6 and ALA 12 versus TYR 16).
    Chain

    NOMATCH 1 (A)
    Correct alignment of ATOM and SEQRES sequences of chain 1 ('A') could not be found by string handling (see 'Parsing methodology' in the text). The raw sequence from the ATOM records is taken to be the true sequence and the SEQRES sequence is discarded.
    Chain

    DUPATOMRES 3
    Multiple sets of coordinates were given for an individual atom or whole residues, first instance on line 3. The first set of coordinates are used and the others discarded.
    Residue

    NOATOMRESID 123
    No atom or residue identifier specified, first instance on line 123. All such lines are discarded.
    Residue

    SEQRESLENDIF 1(A)
    Indicated and actual length of SEQRES sequence differs for chain 1 (chain identifier 'A'). The actual length of the sequence is used.
    Chain

    CHAINIDS 1 (A) 2 (A)
    Chain identifiers of chains 1 and 2 are not unique ('A' in both cases). Both chains are discarded.
    File

    CHAINIDSPC
    Space (' ') and non-space characters are both used for chain identifiers in a single file. Chains in ATOM records are identified by reference to the TER records as well as chain identifiers.
    File

    CHAINORDER 123
    The order of the chains in the ATOM records is inconsistent with that in the SEQRES records, first instance on line 123. Coordinates are assigned to the correct chain by reference to the chain identifier.
    File

    TERNONE
    No TER records were found. The chains in the ATOM records are identified by reference to the chain identifiers.
    File

    TERTOOMANY
    Number of TER records is greater than the number of chains; possible digest.
    File

    TERTOOFEW
    Number of TER records is less than the number of chains.
    File

    TERMISSHET 123 124
    A chain is not separated from its heterogen group by a TER record between lines 123 and 124. Coordinates for the chain and heterogen are distinguished by reference to the chain identifier and residue numbers.
    Chain

    TERMISSCHN 123 124
    Two chains are not separated by TER records between lines 123 and 124.
    Chain

    SEQRESNOAA 1 (A)
    No known amino acids found in the SEQRES records for chain 1 ('A'). The chain is discarded.
    Chain

    SEQRESFEWAA 1 (A)
    Fewer than the user-specified minimum number (5) of known amino acids were found in the SEQRES records for chain 1 ('A'). The chain is discarded.
    Chain

    NOPROTEINS
    No chains were found with at least the user-specified minimum number (5) of known amino acids. The file is not parsed and no output file is generated.
    File

    ATOMFEWAA 1 (A) 3
    Fewer than the user-specified minimum number of known amino acids found in the ATOM records for chain 1 ('A'), model 3. The chain is discarded.
    Chain

    SECMISS 123
    One or more standard records (e.g. for residue identity) were missing for an SSE on line 123. The element(s) are discarded.
    Line

    SECBOTH 1 2 ALA 2 ARG 6
    The start and end residues (ALA 2 ARG 6) of an element given in the HELIX, SHEET or TURN records was not found in the ATOM records of chain 1, model 2. The element is discarded.
    Element

    SECSTART 1 2 ALA 2
    The start residue (ALA 2) of an element was not found in the ATOM records of chain 1, model 2. The element is discarded.
    Element

    SECEND 1 2 ARG 6
    The end residue (ARG 6) of an element was not found in the ATOM records of chain 1, model 2. The element is discarded.
    Element

    SECCHAIN A
    Chain identifier ('A') specified for an element not found in PDB file. The element is discarded.
    Element

    SECTWOCHN A   B
    2 chain identifiers ('A' and 'B') specified for an element. The element is discarded.
    Element

    NOSEQRES
    No SEQRES records. The file is not parsed and no output file is generated.
    File

    NOATOM
    No ATOM records. The file is not parsed and no output file is generated.
    File

    RESOLMOD
    A value for the RESOLUTION record is given but MODEL records are also found. The file is presumed to contain an NMR structure or model.
    File

    NORESOLUTION
    RESOLUTION record not found. The file is presumed to contain an NMR structure or model.
    File

    NOMODEL
    NMR structure with no MODEL records. The number of models is determined by reference to the TER records.
    File

    MODELDUP 123
    Duplicate MODEL records on line 123. The duplicate record is disregarded.
    File

## 13.0 AUTHORS

Jon Ison (jison@rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## 14.0 REFERENCES

Please cite the authors and EMBOSS.
Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

### 14.1 Other useful references

1. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
2. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F.Jr, Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi T. and Tasumi, M. (1997) The Protein Data Bank, a Computer-based Archival File for Macromolecular Structures. J.Mol.Biol. 112, 535-542.
3. Stampf, D.R., Felder, C.E. and Sussman, J.L. PDBbrowse (1995) A graphics interface to the Brookhaven Protein Data Bank. Nature. 374, 572-4
4. Hooft, R.W.W, Vriend, G., Sander, C. and Abola, E.E. (1996) Errors in protein structures. Nature, 381, 272.
5. Bernstein, H, Bernstein, F and Bourne, P.E. pdb2cif: translating PDB entries into mmCIF format. J. Appl. Crystallog., 31, 282-295
6. Brenner, S.E., Koehl, P. and Levitt, M. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
7. Chandonia, J-M., Walker, N.S., Lo Conte, L., Koehl, P., Levitt, M. and Brenner, S.E. (2002) ASTRAL compendium enhancements. Nucleic Acids Res., 30, 260-263.
8. Conte, L.L., Ailey, B., Hubbard, T.J. Brenner, S.E., Murzin, A.G. and Chothia, C. (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res. 28, 257-259.
9. Hamelryck, T. and Manderick, B. PDB file parser and structure class implemented in Python. Bioinformatics. 17, 2308-2310.
10. Frishman, D. and Argos, P. (1996) 75% accuracy in protein secondary structure prediction. Proteins, 27, 329-335
11. Hubbard, S.J. and Thornton, J.M. (1993) 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London.
12. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. and Thornton, J.M. (1997) CATH - A hierarchic classification of protein domain structures. Structure, 5, 1093-1108