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. Parses PDB files and writes protein CCF files


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 residue and atom (RE and AT 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 RE, AT 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 RE or AT records 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 in Figure 2. 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. NCHN is the number of chains that have at least the user-specified minimum number (5) of known amino acids. (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 (with at least the user-specified minimum number (5) of known amino acids), 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 Residue data

Each RE record contains data for a single residue. The data are in 26 columns in the RE record (column numbers are given in parentheses): (1) RE is always given. (2 - 3) Model and chain number (always 1 for domains). (4) Residue number: the position of the residue in the sequence given in the SQ record (for protein atoms) or '.' (for heterogens and water). (5) Original PDB residue number. (6) SSE type from the PDB file: either 'C' (coil), 'H' (helix), 'E' (beta-strand) or 'T' (turn). (7) 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. (8) SSE identifier code from columns 12 - 14 in a HELIX, SHEET or TURN record, or '.' for atoms not in a helix or sheet. (9) 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. (10) Secondary structure assignment according to STRIDE (see Section 11.2). (11) 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. (12) Single character amino acid code or a '.' (for heterogens and water). (13) 3-character residue identifier code. (14-16) Phi and Psi angle and solvent accessible surface area of residue as calculated by STRIDE. (17-26) Accessible surface area according to NACCESS. Absolute and relative measures of accessibility: (17-18) for all atoms, (19-20) all side-chain atoms, (21-22) all main-chain atoms, (23-24) all non-polar side-chain atoms, (25-26) all polar side-chain atoms. Values for records 10-11 and 17-26 are added by using PDBPLUS and a '.' will be given if a value is not available.

4.4 Atom data

Each AT record contains data for a single atom. The data are in 14 columns in the AT record (column numbers are given in parentheses): (1) AT 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) Single character amino acid code or a '.' (for heterogens and water). (8) 3-character residue identifier code. (9) Atom type. (10-12) The x, y and z orthogonal coordinates. (13) Occupancy. (14) Temperature factor.

Output files for usage example

File: pdbparse.log

/homes/user/test/data/structure/1cs4.ent
SEQRESLENDIF   1 (A)
ATOMCOL12      429
BADINDEX       1 (A)
GAPPEDOK       1 (A)
SECSTART       1 1 ILE 384
SECSTART       1 1 ILE 384
//
/homes/user/test/data/structure/1ii7.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
//
/homes/user/test/data/structure/2hhb.ent
ATOMCOL12      1277
//

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;  D8CCAE0E1FC0849A CRC64;
     ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
XX
RE   1    1    2    396   D ASP   .    .    .    .    .    .        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
RE   1    1    3    397   I ILE   .    .    .    .    .    .        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
RE   1    1    4    398   E GLU   .    .    .    .    .    .        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
RE   1    1    5    399   G GLY   1    1    H    1    .    .        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
RE   1    1    6    400   F PHE   1    1    H    1    .    .        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
RE   1    1    7    401   T THR   1    1    H    1    .    .        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
RE   1    1    8    402   S SER   1    1    H    1    .    .        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
RE   1    1    9    403   L LEU   1    1    H    1    .    .        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
RE   1    1    10   404   A ALA   1    1    H    1    .    .        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
RE   1    1    11   405   S SER   1    1    H    1    .    .        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
RE   1    1    12   406   Q GLN   .    .    .    .    .    .        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
RE   1    1    13   407   C CYS   .    .    .    .    .    .        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
RE   1    1    14   408   T THR   2    2    H    1    .    .        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
RE   1    1    15   409   A ALA   2    2    H    1    .    .        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
RE   1    1    16   410   Q GLN   2    2    H    1    .    .        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
RE   1    1    17   411   E GLU   2    2    H    1    .    .        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
RE   1    1    18   412   L LEU   2    2    H    1    .    .        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
RE   1    1    19   413   V VAL   2    2    H    1    .    .        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
RE   1    1    20   414   M MET   2    2    H    1    .    .        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
RE   1    1    21   415   T THR   2    2    H    1    .    .        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
RE   1    1    22   416   L LEU   2    2    H    1    .    .        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
RE   1    1    23   417   N ASN   2    2    H    1    .    .        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
RE   1    1    24   418   E GLU   2    2    H    1    .    .        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
RE   1    1    25   419   L LEU   2    2    H    1    .    .        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
RE   1    1    26   420   F PHE   2    2    H    1    .    .        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
RE   1    1    27   421   A ALA   2    2    H    1    .    .        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
RE   1    1    28   422   R ARG   2    2    H    1    .    .        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
RE   1    1    29   423   F PHE   2    2    H    1    .    .        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
RE   1    1    30   424   D ASP   2    2    H    1    .    .        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
RE   1    1    31   425   K LYS   2    2    H    1    .    .        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
RE   1    1    32   426   L LEU   2    2    H    1    .    .        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
RE   1    1    33   427   A ALA   2    2    H    1    .    .        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
RE   1    1    34   428   A ALA   2    2    H    1    .    .        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
RE   1    1    35   429   E GLU   2    2    H    1    .    .        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
RE   1    1    36   430   N ASN   2    2    H    1    .    .        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]

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

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;   7395 MW;  75FBE75B22FD3678 CRC64;
     MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
     LKKAI
XX
RE   1    1    8    8     D ASP   .    .    .    .    .    .        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
RE   1    1    9    9     I ILE   .    .    .    .    .    .        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
RE   1    1    10   10    H HIS   .    .    .    .    .    .        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
RE   1    1    11   11    L LEU   .    .    .    .    .    .        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
RE   1    1    12   12    G GLY   .    .    .    .    .    .        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
RE   1    1    13   13    Y TYR   .    .    .    .    .    .        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
RE   1    1    14   14    E GLU   1    1    H    5    .    .        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
RE   1    1    15   15    Q GLN   1    1    H    5    .    .        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
RE   1    1    16   16    F PHE   1    1    H    5    .    .        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
RE   1    1    17   17    H HIS   1    1    H    5    .    .        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
RE   1    1    18   18    K LYS   2    A    E    .    .    .        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
RE   1    1    19   19    P PRO   2    A    E    .    .    .        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
RE   1    1    20   20    Q GLN   2    A    E    .    .    .        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
RE   1    1    21   21    R ARG   2    A    E    .    .    .        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
RE   1    1    22   22    E GLU   2    A    E    .    .    .        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
RE   1    1    23   23    E GLU   2    A    E    .    .    .        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
RE   1    1    24   24    E GLU   2    A    E    .    .    .        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
RE   1    1    25   25    F PHE   2    A    E    .    .    .        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
RE   1    1    26   26    A ALA   2    A    E    .    .    .        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
RE   1    1    27   27    E GLU   2    A    E    .    .    .        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
RE   1    1    28   28    A ALA   2    A    E    .    .    .        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
RE   1    1    29   29    F PHE   2    A    E    .    .    .        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
RE   1    1    30   30    K LYS   2    A    E    .    .    .        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
RE   1    1    31   31    N ASN   2    A    E    .    .    .        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
RE   1    1    32   32    A ALA   2    A    E    .    .    .        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
RE   1    1    33   33    L LEU   2    A    E    .    .    .        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
RE   1    1    34   34    E GLU   2    A    E    .    .    .        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
RE   1    1    35   35    I ILE   2    A    E    .    .    .        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
RE   1    1    36   36    A ALA   2    A    E    .    .    .        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
RE   1    1    37   37    V VAL   2    A    E    .    .    .        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
RE   1    1    38   38    Q GLN   2    A    E    .    .    .        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
RE   1    1    39   39    E GLU   2    A    E    .    .    .        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
RE   1    1    40   40    N ASN   .    .    .    .    .    .        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
RE   1    1    41   41    V VAL   .    .    .    .    .    .        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]

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

File: 2hhb.ccf

ID   2hhb
XX
DE   HEMOGLOBIN (DEOXY)
XX
OS   HUMAN (HOMO SAPIENS)
XX
EX   METHOD xray; RESO 1.74; NMOD 1; NCHN 4; NGRP 0;
XX
CN   [1]
XX
IN   ID A; NR 141; NL 1; NH 0; NE 0;
XX
SQ   SEQUENCE   141 AA;  15126 MW;  34D13618E62A33C1 CRC64;
     VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
     KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
     VHASLDKFLA SVSTVLTSKY R
XX
CN   [2]
XX
IN   ID B; NR 146; NL 1; NH 0; NE 0;
XX
SQ   SEQUENCE   146 AA;  15867 MW;  EACBC707CFD466A1 CRC64;
     VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
     KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
     EFTPPVQAAY QKVVAGVANA LAHKYH
XX
CN   [3]
XX
IN   ID C; NR 141; NL 1; NH 0; NE 0;
XX
SQ   SEQUENCE   141 AA;  15126 MW;  34D13618E62A33C1 CRC64;
     VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
     KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
     VHASLDKFLA SVSTVLTSKY R
XX
CN   [4]
XX
IN   ID D; NR 146; NL 2; NH 0; NE 0;
XX
SQ   SEQUENCE   146 AA;  15867 MW;  EACBC707CFD466A1 CRC64;
     VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
     KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
     EFTPPVQAAY QKVVAGVANA LAHKYH
XX
RE   1    1    1    1     V VAL   .    .    .    .    .    .        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
RE   1    1    2    2     L LEU   .    .    .    .    .    .        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
RE   1    1    3    3     S SER   1    AA   H    1    .    .        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
RE   1    1    4    4     P PRO   1    AA   H    1    .    .        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
RE   1    1    5    5     A ALA   1    AA   H    1    .    .        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
RE   1    1    6    6     D ASP   1    AA   H    1    .    .        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]

AT   1    .    .    .    174   . HOH   W O        -4.764   -6.228    5.515    8.00   40.89
AT   1    .    .    .    175   . HOH   W O        23.809   19.925    1.758    8.00   39.37
AT   1    .    .    .    176   . HOH   W O        -7.871   -9.078    2.406    8.00   43.37
AT   1    .    .    .    177   . HOH   W O         4.693   12.083    7.558    8.00   40.24
AT   1    .    .    .    178   . HOH   W O         8.775  -23.438   16.055    8.00   42.33
AT   1    .    .    .    179   . HOH   W O        -7.480  -10.898   17.998    8.00   38.06
AT   1    .    .    .    180   . HOH   W O        -4.731   16.453    2.295    8.00   36.37
AT   1    .    .    .    181   . HOH   W O        -1.055   11.866   -0.448    8.00   43.19
AT   1    .    .    .    182   . HOH   W O       -27.610  -10.991    5.353    8.00   43.46
AT   1    .    .    .    183   . HOH   W O        26.015   11.766    5.159    8.00   40.95
AT   1    .    .    .    184   . HOH   W O       -18.517   -8.355   15.267    8.00   35.55
AT   1    .    .    .    185   . HOH   W O       -14.034    2.806  -30.367    8.00   41.77
AT   1    .    .    .    186   . HOH   W O       -32.905   -9.033    0.480    8.00   43.68
AT   1    .    .    .    187   . HOH   W O       -28.749  -13.315    1.938    8.00   45.36
AT   1    .    .    .    188   . HOH   W O         0.516   -8.074  -26.354    8.00   41.53
AT   1    .    .    .    189   . HOH   W O       -20.080   -9.873  -22.862    8.00   36.25
AT   1    .    .    .    190   . HOH   W O       -13.442    9.778  -13.572    8.00   39.70
AT   1    .    .    .    191   . HOH   W O       -24.804   -2.608  -15.488    8.00   37.79
AT   1    .    .    .    192   . HOH   W O         6.547    9.706   16.296    8.00   41.86
AT   1    .    .    .    193   . HOH   W O         0.029   22.606   14.164    8.00   43.02
AT   1    .    .    .    194   . HOH   W O       -11.367    0.306   28.463    8.00   44.30
AT   1    .    .    .    195   . HOH   W O       -19.950  -10.635   14.301    8.00   40.17
AT   1    .    .    .    196   . HOH   W O        -7.047   -6.324   20.098    8.00   36.98
AT   1    .    .    .    197   . HOH   W O       -23.876    1.108   14.102    8.00   33.31
AT   1    .    .    .    198   . HOH   W O       -34.199    8.033   11.037    8.00   40.72
AT   1    .    .    .    199   . HOH   W O       -14.173   13.393   -8.778    8.00   43.21
AT   1    .    .    .    200   . HOH   W O        11.388  -11.044   24.763    8.00   39.34
AT   1    .    .    .    201   . HOH   W O         3.735   -3.643    2.734    8.00   42.17
AT   1    .    .    .    202   . HOH   W O         3.149   -0.692    2.083    8.00   41.40
AT   1    .    .    .    203   . HOH   W O         4.511  -25.886   13.006    8.00   39.83
AT   1    .    .    .    204   . HOH   W O         8.712  -21.655    3.577    8.00   43.08
AT   1    .    .    .    205   . HOH   W O        22.926   -4.304   24.079    8.00   38.10
AT   1    .    .    .    206   . HOH   W O        11.435    9.654   20.618    8.00   40.23
AT   1    .    .    .    207   . HOH   W O        18.099    5.542   27.744    8.00   39.03
AT   1    .    .    .    208   . HOH   W O        12.174    9.951    9.804    8.00   44.34
AT   1    .    .    .    209   . HOH   W O        24.745   -2.501   15.270    8.00   39.78
AT   1    .    .    .    210   . HOH   W O        24.231    0.100   14.764    8.00   42.94
AT   1    .    .    .    211   . HOH   W O        23.324  -18.136   10.981    8.00   53.60
AT   1    .    .    .    212   . HOH   W O        25.576  -22.211    6.309    8.00   45.18
AT   1    .    .    .    213   . HOH   W O        14.639   24.823   -4.300    8.00   41.35
AT   1    .    .    .    214   . HOH   W O        14.903    5.393  -23.047    8.00   37.45
AT   1    .    .    .    215   . HOH   W O        16.650   -5.137  -16.717    8.00   39.12
AT   1    .    .    .    216   . HOH   W O         7.424   -6.700  -20.085    8.00   38.62
AT   1    .    .    .    217   . HOH   W O        -1.263   -2.837  -21.251    8.00   45.10
AT   1    .    .    .    218   . HOH   W O        23.120   -3.118  -12.992    8.00   37.05
AT   1    .    .    .    219   . HOH   W O        23.664    0.968  -14.389    8.00   36.25
AT   1    .    .    .    220   . HOH   W O        25.698    7.981  -15.362    8.00   35.85
AT   1    .    .    .    221   . HOH   W O        30.009   16.347   -6.794    8.00   37.62
AT   1    .    .    .    222   . HOH   W O        27.728   16.677   -1.376    8.00   42.54
AT   1    .    .    .    223   . HOH   W O         8.142   18.836    1.041    8.00   39.90
//




5.0 DATA FILES

PDBPARSE does not use a data file.


6.0 USAGE 

Parses PDB files and writes protein CCF files.
Version: EMBOSS:6.4.0.0

   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    [N] 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    [N] 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    [N] 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.
   -logfile            outfile    [pdbparse.log] 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    [Y] 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    [5] Minimum number of amino acid residues in
                                  a chain for it to be parsed. (Any integer
                                  value)
   -maxmis             integer    [3] Maximum number of permissible mismatches
                                  between the ATOM and SEQRES sequences. (Any
                                  integer value)
   -maxtrim            integer    [10] Max. no. residues to trim when checking
                                  for missing C-terminal SEQRES sequences.
                                  (Any integer value)

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

   "-pdbpath" associated qualifiers
   -extension1         string     Default file extension

   "-ccfoutdir" associated qualifiers
   -extension2         string     Default file extension

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit

6.1 COMMAND LINE ARGUMENTS

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-pdbpath]
(Parameter 1)		 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. Directory with files ./
-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. Boolean value Yes/No No
-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. Boolean value Yes/No No
-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. Boolean value Yes/No No
[-ccfoutdir]
(Parameter 2)		 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. Output directory ./
-logfile 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. Output file pdbparse.log
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. Boolean value Yes/No Yes
-chnsiz integer Minimum number of amino acid residues in a chain for it to be parsed. Any integer value 5
-maxmis integer Maximum number of permissible mismatches between the ATOM and SEQRES sequences. Any integer value 3
-maxtrim integer Max. no. residues to trim when checking for missing C-terminal SEQRES sequences. Any integer value 10
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-pdbpath" associated dirlist qualifiers
-extension1
-extension_pdbpath		 string Default file extension Any string ent
"-ccfoutdir" associated outdir qualifiers
-extension2
-extension_ccfoutdir		 string Default file extension Any string ccf
"-logfile" associated outfile qualifiers
-odirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 protein CCF files.
Pdb entry directories [./]: 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]: 
Clean protein structure coordinates file output directory [./]: 
Domainatrix log output file [pdbparse.log]: 

Processing /homes/user/test/data/structure/1cs4.ent
Processing /homes/user/test/data/structure/1ii7.ent
Processing /homes/user/test/data/structure/2hhb.ent

Go to the output files for this example






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
PDB file PDB format. Protein coordinate data in PDB format. N.A. N.A.
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 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. 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 amino acid property data from AAINDEX
allversusall Sequence similarity data from all-versus-all comparison
cathparse Generates DCF file from raw CATH files
cutgextract Extract codon usage tables from CUTG database
domainer Generates domain CCF files from protein CCF files
domainnr Removes redundant domains from a DCF file
domainseqs Adds sequence records to a DCF file
domainsse Add secondary structure records to a DCF file
hetparse Converts heterogen group dictionary to EMBL-like format
jaspextract Extract data from JASPAR
pdbplus Add accessibility and secondary structure to a CCF file
pdbtosp Convert swissprot:PDB codes file to EMBL-like format
printsextract Extract data from PRINTS database for use by pscan
prosextract Processes the PROSITE motif database for use by patmatmotifs
rebaseextract Process the REBASE database for use by restriction enzyme applications
scopparse Generate DCF file from raw SCOP files
seqnr Removes redundancy from DHF files
sites Generate residue-ligand CON files from CCF files
ssematch Search a DCF file for secondary structure matches
tfextract Process TRANSFAC transcription factor database for use by tfscan

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@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD 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/ For a publication that uses pdbparse,see for example Journal of Molecular and Cellular Cardiology 40 (2006) 234 - 236

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