INTERFACE 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

Reads CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data. Generate inter-chain CON files from CCF files


2.0 INPUTS & OUTPUTS

INTERFACE reads a protein CCF file (clean coordinate file) and writes a CON file (contacts file) of inter-chain residue-residue contact data. The file contains residue contact data for all pairs of chains in each model in the CCF file. The input and output files are specified by the user. A log file is also written.


3.0 INPUT FILE FORMAT

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

Input files for usage example

File: ../pdbplus-keep/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
//




4.0 OUTPUT FILE FORMAT

The CON format used for the contact files (Figure 1) is similar to EMBL format and is described in the CONTACTS documentation. A few of the records differ in the INTERFACE output compared to the CONTACTS output, however, so for the sake of clarity all records are described below.

Output files for usage example

File: 2hhb.con

XX   Inter-chain residue-residue contact data.
XX
TY   INTER
XX
EX   THRESH 1.0; IGNORE 20.0; NMOD 1; NCHA 4
XX
NE   6
XX
EN   [1]
XX
ID   PDB 2hhb; DOM .; LIG .
XX
CN   MO 1; CN1 1; CN2 2; ID1 A; ID2 B; NRES1 141; NRES2 146
XX
S1   SEQUENCE   141 AA;  15126 MW;  34D13618E62A33C1 CRC64;
     VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
     KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
     VHASLDKFLA SVSTVLTSKY R
XX
S2   SEQUENCE   146 AA;  15867 MW;  EACBC707CFD466A1 CRC64;
     VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
     KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
     EFTPPVQAAY QKVVAGVANA LAHKYH
XX
NC   SM 48; LI .
XX
SM   GLU 30 ; PRO 124
SM   ARG 31 ; PHE 122
SM   ARG 31 ; THR 123
SM   ARG 31 ; PRO 124
SM   ARG 31 ; GLN 127
SM   LEU 34 ; PRO 124
SM   LEU 34 ; PRO 125
SM   LEU 34 ; ALA 128
SM   SER 35 ; GLN 127
SM   SER 35 ; ALA 128
SM   SER 35 ; GLN 131
SM   PHE 36 ; GLN 131
SM   HIS 103 ; ASN 108
SM   HIS 103 ; VAL 111
SM   HIS 103 ; CYS 112
SM   HIS 103 ; GLN 127
SM   HIS 103 ; GLN 131
SM   CYS 104 ; GLN 127
SM   LEU 106 ; CYS 112
SM   VAL 107 ; VAL 111
SM   VAL 107 ; CYS 112
SM   VAL 107 ; ALA 115
SM   VAL 107 ; PHE 122
SM   VAL 107 ; GLN 127


  [Part of this file has been deleted for brevity]

SM   GLU 27 ; PRO 124
SM   GLU 30 ; PRO 124
SM   ARG 31 ; PHE 122
SM   ARG 31 ; THR 123
SM   ARG 31 ; PRO 124
SM   ARG 31 ; GLN 127
SM   LEU 34 ; PRO 124
SM   LEU 34 ; PRO 125
SM   LEU 34 ; ALA 128
SM   SER 35 ; GLN 127
SM   SER 35 ; ALA 128
SM   SER 35 ; GLN 131
SM   PHE 36 ; GLN 131
SM   HIS 103 ; ASN 108
SM   HIS 103 ; VAL 111
SM   HIS 103 ; CYS 112
SM   HIS 103 ; GLN 127
SM   HIS 103 ; GLN 131
SM   CYS 104 ; GLN 127
SM   LEU 106 ; CYS 112
SM   VAL 107 ; VAL 111
SM   VAL 107 ; CYS 112
SM   VAL 107 ; ALA 115
SM   VAL 107 ; PHE 122
SM   VAL 107 ; GLN 127
SM   ALA 110 ; CYS 112
SM   ALA 110 ; ALA 115
SM   ALA 110 ; HIS 116
SM   ALA 111 ; ALA 115
SM   ALA 111 ; GLY 119
SM   LEU 113 ; HIS 116
SM   PRO 114 ; HIS 116
SM   PHE 117 ; ARG 30
SM   PHE 117 ; CYS 112
SM   PHE 117 ; HIS 116
SM   THR 118 ; ARG 30
SM   PRO 119 ; ARG 30
SM   PRO 119 ; VAL 33
SM   PRO 119 ; VAL 34
SM   PRO 119 ; MET 55
SM   ALA 120 ; VAL 33
SM   ALA 120 ; PRO 51
SM   HIS 122 ; ARG 30
SM   HIS 122 ; VAL 34
SM   HIS 122 ; VAL 109
SM   HIS 122 ; CYS 112
SM   ALA 123 ; VAL 33
SM   ALA 123 ; VAL 34
SM   ASP 126 ; VAL 34
SM   ASP 126 ; TYR 35
//

File: interface.log

2hhb




5.0 DATA FILES

INTERFACE uses a data file containing van der Waals radii for atoms in proteins (see CONTACTS documentation.) The file Evdw.dat is such a data file and is part of the EMBOSS distribution.


6.0 USAGE

Generate inter-chain CON files from CCF files.
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            infile     This option specifies the name of the
                                  protein CCF file (clean coordinate file)
                                  (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.
   -thresh             float      [1.0] This option specifies the threshold
                                  contact distance. Contact between two
                                  residues is defined as when the van der
                                  Waals surface of any atom of the first
                                  residue comes within the threshold contact
                                  distance of the van der Waals surface of any
                                  atom of the second residue. The threshold
                                  contact distance is a user-defined distance
                                  with a default value of 1 Angstrom. (Any
                                  numeric value)
  [-outfile]           outfile    [test.con] This option specifies the name of
                                  CON file (contact file) (output). A
                                  'contact file' contains contact data for a
                                  protein or a domain from SCOP or CATH, in
                                  the CON format (EMBL-like). The contacts may
                                  be intra-chain residue-residue, inter-chain
                                  residue-residue or residue-ligand. The
                                  files are generated by using CONTACTS,
                                  INTERFACE and SITES.
   -conlogfile         outfile    [interface.log] This option specifies the
                                  name of the log file for the build. The log
                                  file contains messages about any errors
                                  arising while INTERFACE ran.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -vdwfile            datafile   [Evdw.dat] This option specifies the name of
                                  data file with van der Waals radii. The
                                  file of van der Waals radii for atoms in
                                  amino acid residues is part of the emboss
                                  distribution.
   -ignore             float      [20.0] This option specifies the threshold
                                  ignore distance. If any two atoms from two
                                  different residues are at least this
                                  distance apart then no futher inter-atomic
                                  contacts will be checked for for that
                                  residue pair . This speeds the calculation
                                  up considerably. (Any numeric value)

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-conlogfile" 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
[-infile]
(Parameter 1)
infile This option specifies the name of the protein CCF file (clean coordinate file) (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. Input file Required
-thresh float This option specifies the threshold contact distance. Contact between two residues is defined as when the van der Waals surface of any atom of the first residue comes within the threshold contact distance of the van der Waals surface of any atom of the second residue. The threshold contact distance is a user-defined distance with a default value of 1 Angstrom. Any numeric value 1.0
[-outfile]
(Parameter 2)
outfile This option specifies the name of CON file (contact file) (output). A 'contact file' contains contact data for a protein or a domain from SCOP or CATH, in the CON format (EMBL-like). The contacts may be intra-chain residue-residue, inter-chain residue-residue or residue-ligand. The files are generated by using CONTACTS, INTERFACE and SITES. Output file test.con
-conlogfile outfile This option specifies the name of the log file for the build. The log file contains messages about any errors arising while INTERFACE ran. Output file interface.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-vdwfile datafile This option specifies the name of data file with van der Waals radii. The file of van der Waals radii for atoms in amino acid residues is part of the emboss distribution. Data file Evdw.dat
-ignore float This option specifies the threshold ignore distance. If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair . This speeds the calculation up considerably. Any numeric value 20.0
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile
string Output directory Any string  
"-conlogfile" 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 INTERFACE is shown below. Here is a sample session with interface


% interface 
Generate inter-chain CON files from CCF files.
Clean protein structure coordinates file: ../pdbplus-keep/2hhb.ccf
Threshold contact distance [1.0]: 1
Structure contacts output file [test.con]: 2hhb.con
Domainatrix log output file [interface.log]: 

2hhb

Go to the input files for this example
Go to the output files for this example




7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

Types of contact
SM records are used for contacts between either either side-chain or main-chain atoms as defined above. In a future implementation, SS will be used for side-chain only contacts, MM will be used for main-chain only contacts, LI will be used for contacts to ligands, and there will probably be several other forms of contact too.

Threshold ignore distance option
The threshold ignore distance can be adjusted to speed-up the calculation of contacts considerably. If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair.

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.
Contact file (intra-chain residue-residue contacts) CON format (EMBL-like.) Intra-chain residue-residue contact data for a protein or a domain from SCOP or CATH. CONTACTS N.A.
Contact file (inter-chain residue-residue contacts) CON format (EMBL-like.) Inter-chain residue-residue contact data for a protein or a domain from SCOP or CATH. INTERFACE N.A.
Contact file (residue-ligand contacts) CON format (EMBL-like.) Residue-ligand contact data for a protein or a domain from SCOP or CATH. SITES N.A.
van der Waals radii A file of van der Waals radii for atoms in amino acid residues. Part of the emboss distribution. N.A. N.A.
None


9.0 DESCRIPTION

Knowledge of the physical contacts that amino acid residues in two different polypeptide chains of a protein make with one another is required for several different analyses. INTERFACE calculates inter-chain residue-residue contact data from protein CCF files (clean coordinate files).


10.0 ALGORITHM

Contact between two residues is defined as when the van der Waals surface of any atom of the first residue comes within the threshold contact distance of the van der Waals surface of any atom of the second residue. The threshold contact distance is a user-defined distance with a default value of 1 Angstrom.


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



12.0 DIAGNOSTIC ERROR MESSAGES

INTERFACE generates a log file an excerpt of which is shown below. If there is a problem in processing a CCF file, three lines containing the record '//', the PDB identifier code and an error message respectively are written. The text 'WARN file open error filename' , 'ERROR file read error filename' or 'ERROR file write error filename ' will be reported when an error was encountered during a file open, read or write respectively. Various other error messages may also be given (in case of difficulty email Jon Ison, jison@ebi.ac.uk).


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/

14.1 Other useful references