| ## PDBPLUS 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

## 2.0 INPUTS & OUTPUTS

PDBPLUS reads a directory of domain OR protein CCF files (clean coordinate files) and writes a directory containing the same files as the input directory but in which values for records for secondary structure and residue accessibility are given. These data are calculated by using the STRIDE and NACCESS programs and these must be installed on the system that is running PDBPLUS (see Section 8.0 below). PDBPLUS also requires a directory containing files in PDB format for each coordinate file in the input directory: either the original PDB file (for proteins) or domain PDB files generated by using DOMAINER (for domains). The paths and extensions of the pdb (input) and coordinate (input and output) files are specified by the user (file extensions are given in the ACD file). The names of the output CCF files will be identical to those that are read.
PDBPLUS generates 3 log files containing diagnostic messages for various problems encountered by PDBPARSE, STRIDE or NACCESS respectively (see Section 12.0 below).

## 3.0 INPUT FILE FORMAT

The format of the CCF file is described in the PDBPARSE documentation.

## 4.0 OUTPUT FILE FORMAT

The format of the CCF file is described in the PDBPARSE documentation.

### Output files for usage example

### File: pdbplus.log

    stride output for: /homes/user/test/data/structure/1cs4.ent
    //
    stride data for: /homes/user/test/data/structure/1cs4.ent
    //
    naccess output for: /homes/user/test/data/structure/1cs4.ent
    //
    naccess data for: /homes/user/test/data/structure/1cs4.ent
    //
    stride output for: /homes/user/test/data/structure/1ii7.ent
    //
    stride data for: /homes/user/test/data/structure/1ii7.ent
    //
    naccess output for: /homes/user/test/data/structure/1ii7.ent
    //
    naccess data for: /homes/user/test/data/structure/1ii7.ent
    //
    stride output for: /homes/user/test/data/structure/2hhb.ent
    //
    stride data for: /homes/user/test/data/structure/2hhb.ent
    //
    naccess output for: /homes/user/test/data/structure/2hhb.ent
    //
    naccess data for: /homes/user/test/data/structure/2hhb.ent
    //

    STRIDE  failures: 0
    NACCESS failures: 0

### File: stride.log

### File: naccess.log

    naccess: using defualt vdw.radii
    naccess: using default STD FILE
    naccess: using defualt vdw.radii
    naccess: using default STD FILE
    naccess: using defualt vdw.radii
    naccess: using default STD FILE

### 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 2; 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   .    .    .    .    .    C      360.00  138.76  146.70  139.38   99.30   65.52   63.80   73.85  195.90   37.10   75.30  102.28  112.20
    RE   1    1    3    397   I ILE   .    .    .    .    .    T      -70.66  130.71   41.60   42.25   24.10   39.03   28.30    3.22    8.70   39.03   28.10    3.22    9.00
    RE   1    1    4    398   E GLU   .    .    .    .    .    T      -80.63  128.14  189.80  172.42  100.10  152.25  113.00   20.18   53.80   71.11  118.00  101.31   90.50
    RE   1    1    5    399   G GLY   1    1    H    1    .    T       60.62   44.06   47.30   46.32   57.80   33.67  104.20   12.64   26.50   33.67   89.70   12.64   29.70
    RE   1    1    6    400   F PHE   1    1    H    1    1    H      -63.71  -43.06   38.10   42.33   21.20   38.88   23.70    3.46    9.80   38.88   23.50    3.46   10.10
    RE   1    1    7    401   T THR   1    1    H    1    1    H      -63.13  -33.45  122.50  117.00   84.00  113.46  111.60    3.54    9.40   81.54  107.70   35.46   55.80
    RE   1    1    8    402   S SER   1    1    H    1    1    H      -69.61  -44.64   76.80   69.25   59.40   66.11   84.60    3.14    8.20   36.50   75.20   32.75   48.20
    RE   1    1    9    403   L LEU   1    1    H    1    1    H      -63.95  -53.38   81.30   81.72   45.70   81.25   57.60    0.47    1.30   81.25   57.10    0.47    1.30
    RE   1    1    10   404   A ALA   1    1    H    1    1    H      -67.72  -13.25   35.90   35.58   33.00   16.63   24.00   18.95   49.20   18.20   25.50   17.38   47.50
    RE   1    1    11   405   S SER   1    1    H    1    .    T      -82.48  -15.19  100.90   90.08   77.30   61.12   78.20   28.96   75.40   25.90   53.40   64.18   94.40
    RE   1    1    12   406   Q GLN   .    .    .    .    .    T      -95.87  -61.03  151.90  142.66   79.90  109.97   78.00   32.69   87.10   49.16   94.10   93.49   74.00
    RE   1    1    13   407   C CYS   .    .    .    .    .    T      -79.87  165.96   32.00   36.35   27.10   27.88   28.80    8.47   22.60   29.04   29.70    7.31   20.10
    RE   1    1    14   408   T THR   2    2    H    1    .    C      -67.21  155.23   79.50   78.09   56.10   73.27   72.00    4.82   12.80   53.17   70.20   24.92   39.20
    RE   1    1    15   409   A ALA   2    2    H    1    2    H      -61.46  -26.61   74.80   80.21   74.30   71.49  103.00    8.72   22.60   72.91  102.10    7.31   20.00
    RE   1    1    16   410   Q GLN   2    2    H    1    2    H      -69.67  -54.28  138.50  127.16   71.20  124.25   88.10    2.91    7.80   46.24   88.60   80.92   64.10
    RE   1    1    17   411   E GLU   2    2    H    1    2    H      -57.11  -42.09  104.70   89.88   52.20   89.35   66.30    0.53    1.40   31.77   52.70   58.11   51.90
    RE   1    1    18   412   L LEU   2    2    H    1    2    H      -57.70  -47.91   25.70   25.00   14.00   25.00   17.70    0.00    0.00   25.00   17.60    0.00    0.00
    RE   1    1    19   413   V VAL   2    2    H    1    2    H      -66.05  -30.11   88.20   90.90   60.00   90.80   79.50    0.10    0.30   90.90   78.70    0.00    0.00
    RE   1    1    20   414   M MET   2    2    H    1    2    H      -69.27  -42.21  124.20  127.92   65.90  122.84   78.40    5.08   13.50  124.37   78.80    3.54    9.80
    RE   1    1    21   415   T THR   2    2    H    1    2    H      -65.51  -37.49   81.70   78.15   56.10   76.18   74.90    1.96    5.20   56.58   74.70   21.56   33.90
    RE   1    1    22   416   L LEU   2    2    H    1    2    H      -74.87  -41.05   26.30   23.57   13.20   23.31   16.50    0.26    0.70   23.57   16.60    0.00    0.00
    RE   1    1    23   417   N ASN   2    2    H    1    2    H      -67.86  -35.26  113.60  101.30   70.40   99.87   94.00    1.43    3.80   18.39   39.80   82.91   84.80
    RE   1    1    24   418   E GLU   2    2    H    1    2    H      -65.83  -40.82  113.30  100.53   58.40   99.74   74.00    0.79    2.10   38.76   64.30   61.77   55.20
    RE   1    1    25   419   L LEU   2    2    H    1    2    H      -72.73  -52.39   57.40   57.47   32.20   57.33   40.60    0.14    0.40   57.33   40.30    0.14    0.40
    RE   1    1    26   420   F PHE   2    2    H    1    2    H      -70.80  -21.35   27.00   28.81   14.40   27.76   16.90    1.06    3.00   28.81   17.40    0.00    0.00
    RE   1    1    27   421   A ALA   2    2    H    1    2    H      -69.34  -45.28   29.90   35.82   33.20   34.83   50.20    1.00    2.60   34.83   48.80    1.00    2.70
    RE   1    1    28   422   R ARG   2    2    H    1    2    H      -61.82  -45.79  136.10  134.66   56.40  134.62   66.90    0.03    0.10   47.36   60.90   87.30   54.20
    RE   1    1    29   423   F PHE   2    2    H    1    2    H      -57.44  -43.57  101.50   99.54   49.90   95.45   58.20    4.09   11.60   96.26   58.30    3.28    9.60
    RE   1    1    30   424   D ASP   2    2    H    1    2    H      -62.18  -31.31   60.50   54.34   38.70   42.49   41.40   11.84   31.40   25.02   50.80   29.31   32.20
    RE   1    1    31   425   K LYS   2    2    H    1    2    H      -78.40  -41.15  135.60  131.47   65.50  129.94   79.60    1.53    4.10   94.19   80.80   37.29   44.30
    RE   1    1    32   426   L LEU   2    2    H    1    2    H      -64.72  -26.22   81.20   86.96   48.70   86.30   61.20    0.66    1.80   86.96   61.10    0.00    0.00
    RE   1    1    33   427   A ALA   2    2    H    1    2    H      -69.69  -37.04   17.80   18.88   17.50   18.70   26.90    0.18    0.50   18.70   26.20    0.18    0.50
    RE   1    1    34   428   A ALA   2    2    H    1    2    H      -70.19  -38.47   77.30   79.34   73.50   60.25   86.80   19.09   49.50   61.54   86.20   17.79   48.60
    RE   1    1    35   429   E GLU   2    2    H    1    2    H      -66.66  -43.34  133.10  123.38   71.60  108.84   80.80   14.54   38.80   51.79   85.90   71.59   63.90
    RE   1    1    36   430   N ASN   2    2    H    1    2    H      -85.82   10.44  105.20   96.15   66.80   83.39   78.50   12.75   33.80   21.86   47.30   74.28   76.00

      [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 1; 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   .    .    .    .    .    C      360.00   53.69  128.30  117.77   83.90   84.46   82.20   33.31   88.40   34.39   69.80   83.38   91.50
    RE   1    1    9    9     I ILE   .    .    .    .    .    C      -72.50  -37.00   42.90   42.38   24.20   41.07   29.80    1.31    3.50   41.07   29.50    1.31    3.60
    RE   1    1    10   10    H HIS   .    .    .    .    .    T       50.63   45.81   76.20   75.98   41.50   75.67   51.40    0.31    0.90   48.67   50.10   27.31   31.90
    RE   1    1    11   11    L LEU   .    .    .    .    .    T      -57.60  139.21   78.50   79.58   44.50   55.49   39.30   24.09   64.20   56.43   39.70   23.15   63.70
    RE   1    1    12   12    G GLY   .    .    .    .    .    T       91.01   -4.77   47.80   51.11   63.80   23.22   71.80   27.90   58.40   27.09   72.10   24.02   56.50
    RE   1    1    13   13    Y TYR   .    .    .    .    .    T      -74.99  115.31  107.80  100.62   47.30  100.09   56.40    0.52    1.50   66.13   48.50   34.48   45.20
    RE   1    1    14   14    E GLU   1    1    H    5    .    C      -96.17   74.41   82.00   71.84   41.70   61.45   45.60   10.39   27.70   17.84   29.60   54.00   48.20
    RE   1    1    15   15    Q GLN   1    1    H    5    .    G      -56.45  130.81   34.70   33.39   18.70   33.39   23.70    0.00    0.00    0.31    0.60   33.08   26.20
    RE   1    1    16   16    F PHE   1    1    H    5    .    G       57.56   29.90  146.10  150.86   75.60  136.18   83.00   14.68   41.50  136.40   82.50   14.46   42.20
    RE   1    1    17   17    H HIS   1    1    H    5    .    G       55.61   29.81  160.00  158.76   86.80  143.03   97.20   15.72   43.90   93.02   95.70   65.74   76.70
    RE   1    1    18   18    K LYS   2    A    E    .    .    C     -111.48  108.83  115.50  109.57   54.60  109.57   67.10    0.00    0.00   67.34   57.80   42.23   50.10
    RE   1    1    19   19    P PRO   2    A    E    .    1    H      -54.76  -17.53   74.50   83.79   61.60   82.99   69.20    0.80    4.90   82.99   68.60    0.80    5.30
    RE   1    1    20   20    Q GLN   2    A    E    .    1    H      -73.35  -35.75  120.10  112.90   63.30  111.79   79.30    1.11    3.00   28.62   54.80   84.28   66.70
    RE   1    1    21   21    R ARG   2    A    E    .    1    H      -68.53  -38.89   82.60   84.22   35.30   84.22   41.80    0.00    0.00   22.91   29.40   61.31   38.10
    RE   1    1    22   22    E GLU   2    A    E    .    1    H      -56.60  -42.19   71.00   59.66   34.60   59.41   44.10    0.25    0.70   17.46   29.00   42.20   37.70
    RE   1    1    23   23    E GLU   2    A    E    .    1    H      -66.34  -36.55  123.60  108.67   63.10  104.55   77.60    4.12   11.00   54.20   89.90   54.47   48.60
    RE   1    1    24   24    E GLU   2    A    E    .    1    H      -71.24  -35.34   80.40   71.99   41.80   67.32   50.00    4.67   12.40   41.76   69.30   30.23   27.00
    RE   1    1    25   25    F PHE   2    A    E    .    1    H      -63.59  -40.62   41.80   41.19   20.60   39.81   24.30    1.38    3.90   39.81   24.10    1.38    4.00
    RE   1    1    26   26    A ALA   2    A    E    .    1    H      -66.25  -43.69   46.10   46.40   43.00   41.37   59.60    5.03   13.10   42.55   59.60    3.85   10.50
    RE   1    1    27   27    E GLU   2    A    E    .    1    H      -60.95  -39.89   91.00   84.33   49.00   83.96   62.30    0.36    1.00   41.68   69.10   42.65   38.10
    RE   1    1    28   28    A ALA   2    A    E    .    1    H      -58.03  -47.16   55.00   58.08   53.80   52.98   76.30    5.10   13.20   54.38   76.20    3.70   10.10
    RE   1    1    29   29    F PHE   2    A    E    .    1    H      -61.12  -42.56   38.50   33.87   17.00   33.36   20.30    0.51    1.40   33.36   20.20    0.51    1.50
    RE   1    1    30   30    K LYS   2    A    E    .    1    H      -63.44  -42.40  104.70  105.98   52.80  105.45   64.60    0.53    1.40   58.41   50.10   47.56   56.50
    RE   1    1    31   31    N ASN   2    A    E    .    1    H      -60.26  -47.05   77.00   73.22   50.90   72.53   68.30    0.70    1.80   23.06   49.90   50.16   51.30
    RE   1    1    32   32    A ALA   2    A    E    .    1    H      -58.51  -48.57   56.20   56.15   52.00   49.87   71.80    6.28   16.30   51.18   71.70    4.97   13.60
    RE   1    1    33   33    L LEU   2    A    E    .    1    H      -61.69  -37.59   59.70   59.93   33.60   59.56   42.20    0.38    1.00   59.93   42.10    0.00    0.00
    RE   1    1    34   34    E GLU   2    A    E    .    1    H      -68.18  -35.02   87.40   76.92   44.70   76.19   56.50    0.74    2.00   33.77   56.00   43.15   38.50
    RE   1    1    35   35    I ILE   2    A    E    .    1    H      -69.89  -35.85   89.80   96.84   55.30   96.84   70.20    0.00    0.00   96.84   69.60    0.00    0.00
    RE   1    1    36   36    A ALA   2    A    E    .    1    H      -61.30  -45.01   19.20   19.50   18.10   19.22   27.70    0.27    0.70   19.22   26.90    0.27    0.70
    RE   1    1    37   37    V VAL   2    A    E    .    1    H      -64.92  -44.30  109.50  111.45   73.60  102.58   89.80    8.87   23.90  102.58   88.80    8.87   24.70
    RE   1    1    38   38    Q GLN   2    A    E    .    1    H      -59.93  -32.77  145.80  140.48   78.70  113.02   80.20   27.46   73.20   49.34   94.50   91.14   72.20
    RE   1    1    39   39    E GLU   2    A    E    .    1    H      -83.49    5.97  133.40  118.49   68.80   99.06   73.50   19.43   51.80   31.08   51.60   87.41   78.10
    RE   1    1    40   40    N ASN   .    .    .    .    .    C       54.97   43.05  136.50  126.77   88.10  116.79  109.90    9.98   26.50   31.92   69.00   94.86   97.10
    RE   1    1    41   41    V VAL   .    .    .    .    .    C      -70.50  156.23   65.90   69.23   45.70   50.82   44.50   18.40   49.50   50.86   44.00   18.36   51.10

      [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 7; 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 8; 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 7; 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 8; 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   .    .    .    .    .    C      360.00  130.57  137.00  142.86   94.30  113.45   99.30   29.40   79.10  113.56   98.30   29.29   81.40
    RE   1    1    2    2     L LEU   .    .    .    .    .    C      -80.50  121.94   16.80   18.20   10.20    7.73    5.50   10.48   27.90    7.73    5.40   10.48   28.80
    RE   1    1    3    3     S SER   1    AA   H    1    .    C      -71.32  164.78   44.40   44.59   38.30   44.42   56.90    0.17    0.40   39.26   80.90    5.34    7.90
    RE   1    1    4    4     P PRO   1    AA   H    1    1    H      -62.31  -35.05   99.60  105.25   77.30  103.02   85.90    2.23   13.70  103.65   85.70    1.60   10.50
    RE   1    1    5    5     A ALA   1    AA   H    1    1    H      -65.00  -41.52   59.80   65.59   60.80   64.35   92.70    1.24    3.20   64.35   90.20    1.24    3.40
    RE   1    1    6    6     D ASP   1    AA   H    1    1    H      -56.29  -42.84   13.60   13.83    9.90   13.80   13.40    0.03    0.10    0.44    0.90   13.39   14.70

      [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

PDBPLUS does not use a data file.

## 6.0 USAGE

    Add accessibility and secondary structure to a CCF file.
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-ccfinpath]         dirlist    [./] This option specifies the location of
                                      CCF files (clean coordinate files) (input).
                                      A 'clean cordinate file' contains protein
                                      coordinate and derived data for a single PDB
                                      file ('protein clean coordinate file') or a
                                      single domain from SCOP or CATH ('domain
                                      clean coordinate file'), in CCF format
                                      (EMBL-like). The files, generated by using
                                      PDBPARSE (PDB files) or DOMAINER (domains),
                                      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.
      [-pdbindir]          directory  [./] 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
       -pdbprefix          string     This option specifies the file prefix of PDB
                                      files (if any) (Any string)
       -mode               menu       [1] This option specifies the mode of
                                      operation. (Values: 1 (Use STRIDE only); 2
                                      (Use NACCESS only); 3 (Use STRIDE and
                                      NACCESS))
    *  -thresholdsize      integer    [4] This option specifies the threshold size
                                      for SSEs (secondary structure elements)
                                      (Any integer value)
      [-ccfoutdir]         outdir     [./] This option specifies the location of
                                      CCF files (clean coordinate files) (output).
                                      A 'clean cordinate file' contains protein
                                      coordinate and derived data for a single PDB
                                      file ('protein clean coordinate file') or a
                                      single domain from SCOP or CATH ('domain
                                      clean coordinate file'), in CCF format
                                      (EMBL-like). The files, generated by using
                                      PDBPARSE (PDB files) or DOMAINER (domains),
                                      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    [pdbplus.log] This option specifies the name
                                      of the log file for PDBPLUS
    *  -slogfile           outfile    [stride.log] This option specifies the name
                                      of the log file for STRIDE
    *  -nlogfile           outfile    [naccess.log] This option specifies the name
                                      of the log file for NACCESS

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

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

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

       "-ccfoutdir" associated qualifiers
       -extension3         string     Default file extension

       "-logfile" associated qualifiers
       -odirectory         string     Output directory

       "-slogfile" associated qualifiers
       -odirectory         string     Output directory

       "-nlogfile" 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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-ccfinpath] (Parameter 1) | dirlist | This option specifies the location of CCF files (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), 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. | Directory with files | ./
[-pdbindir] (Parameter 2) | directory | 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 | ./
-pdbprefix | string | This option specifies the file prefix of PDB files (if any) | Any string |
-mode | list | This option specifies the mode of operation. |
1 | (Use STRIDE only)
2 | (Use NACCESS only)
3 | (Use STRIDE and NACCESS)
| 1
-thresholdsize | integer | This option specifies the threshold size for SSEs (secondary structure elements) | Any integer value | 4
[-ccfoutdir] (Parameter 3) | outdir | This option specifies the location of CCF files (clean coordinate files) (output). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), 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 the name of the log file for PDBPLUS | Output file | pdbplus.log
-slogfile | outfile | This option specifies the name of the log file for STRIDE | Output file | stride.log
-nlogfile | outfile | This option specifies the name of the log file for NACCESS | Output file | naccess.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-ccfinpath" associated dirlist qualifiers
-extension1 -extension_ccfinpath | string | Default file extension | Any string | ccf
"-pdbindir" associated directory qualifiers
-extension2 -extension_pdbindir | string | Default file extension | Any string | ent
"-ccfoutdir" associated outdir qualifiers
-extension3 -extension_ccfoutdir | string | Default file extension | Any string | ccf
"-logfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-slogfile" associated outfile qualifiers
-odirectory | string | Output directory | Any string |
"-nlogfile" 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 PDBPLUS is shown below. Here is a sample session with pdbplus

    % pdbplus
    Add accessibility and secondary structure to a CCF file.
    Clean protein structure coordinates directories [./]: ../pdbparse-keep/
    Pdb entry directory [./]:
    File prefix of PDB files (if any):
    Mode of operation
             1 : Use STRIDE only
             2 : Use NACCESS only
             3 : Use STRIDE and NACCESS
    Select mode [1]: 3
    Threshold size for SSEs (secondary structure elements) [4]: 4
    Clean protein structure coordinates file output directory [./]:
    Domainatrix log output file [pdbplus.log]:
    Stride program log output file [stride.log]:
    Naccess program log output file [naccess.log]:

    Processing /homes/user/test/qa/pdbparse-keep/1cs4.ccf
    /shared/software/bin/stride /homes/user/test/data/structure/1cs4.ent -f./pdbplus-1234567890.1234
    /shared/software/bin/naccess /homes/user/test/data/structure/1cs4.ent
    Processing /homes/user/test/qa/pdbparse-keep/1ii7.ccf
    /shared/software/bin/stride /homes/user/test/data/structure/1ii7.ent -f./pdbplus-1234567890.1234
    /shared/software/bin/naccess /homes/user/test/data/structure/1ii7.ent
    Processing /homes/user/test/qa/pdbparse-keep/2hhb.ccf
    /shared/software/bin/stride /homes/user/test/data/structure/2hhb.ent -f./pdbplus-1234567890.1234
    /shared/software/bin/naccess /homes/user/test/data/structure/2hhb.ent
    STRIDE  failures: 0
    NACCESS failures: 0

Go to the output files for this example

## 7.0 KNOWN BUGS & WARNINGS

NACCESS and STRIDE do not always work as advertised owing, e.g. to arbitrary array limits in their code. If the derived data appears to be missing from the PDDBPARSE output this is probably why.

## 8.0 NOTES

PDBPLUS requires a working version of NACCESS and STRIDE.

### 8.1 GLOSSARY OF FILE TYPES

FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO
Clean coordinate file (for protein) | CCF format (EMBL-like). | Protein coordinate and derived 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.
Clean coordinate file (for domain) | CCF format (EMBL-like). | Protein coordinate and derived data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.
PDB file | PDB format. | Protein coordinate data in PDB format. | N.A. | N.A.
Domain PDB file | PDB format. | Protein coordinate data for a single domain from SCOP or CATH. | DOMAINER | N.A.

None

## 9.0 DESCRIPTION

PDBPLUS is a wrapper to the STRIDE [1] and NACCESS [2] programs that adds derived data (i - iv below) to a CCF file. 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, i.e. whether PDBPLUS is provided with protein or domain CCF files. Thus PDBPLUS provides useful flexibility in generating the derived data.

- 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.
- Phi and Psi angle and solvent accessible surface area of residues as calculated by using STRIDE.
- 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).
- 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).

## 10.0 ALGORITHM

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). PDBPLUS is used to assign values to these these records.

## 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 | Generate DCF file from raw CATH files
cutgextract | Extract codon usage tables from CUTG database
domainer | Generate domain CCF files from protein CCF files
domainnr | Remove redundant domains from a DCF file
domainseqs | Add sequence records to a DCF file
domainsse | Add secondary structure records to a DCF file
hetparse | Convert heterogen group dictionary to EMBL-like format
jaspextract | Extract data from JASPAR
pdbparse | Parse PDB files and writes protein CCF files
pdbtosp | Convert swissprot:PDB codes file to EMBL-like format
printsextract | Extract data from PRINTS database for use by pscan
prosextract | Process 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 | Remove 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

## 12.0 DIAGNOSTIC ERROR MESSAGES

The following messages (in "quotes") may appear in the PDBPARSE log file (an explanation is given in parenethesis).

- "clean coordinate file not found my.file" (a clean coordinate input file was not found for input)
- "ERROR Clean coordinate file read error: my.file" (error in reading clean coordinate file)
- "no stride output for: my.file" (No STRIDE output was generated for my.file)
- "stride output for: my.file" (STRIDE output *was* generated for my.file)
- "no naccess output for:" (No NACCESS output was generated for my.file)
- "naccess output for:" (NACCESS output *was* generated for my.file)
- "PDB file not found: my.file" (a pdb file was not found for input)
- "Could not write results file: my.file" (output file could not be written)
- "Could not convert chain id A to chain number in pdb file my.file" (chain identifier was not found in the clean coordinate file)
- "STRIDE failures: %12\nNACCESS failures: 123" (STRIDE failed for 12 pdb files and NACCESS failed for 123 pdb files. The clean coordinate files will lack the appropriate data (see Section 10.0).

## 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. 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. Frishman, D. & Argos, P. (1995).  Knowledge-Based Secondary Structure Assignment.  Proteins 23:566-579.

    2. Hubbard,S.J. & Thornton, J.M. (1993), 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London.