| ## MATGEN3D 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

Generate a 3D-1D scoring matrix from CCF files

Generates a 3D-1D scoring matrix from CCF files (clean coordinate files).

## 2.0 INPUTS & OUTPUTS

MATGEN3D reads a DCF file (domain classification file) and a directory of domain CCF files (clean coordinate files) which have been processed by using PDBPLUS so that they contain solvent accessibility and secondary structure information. The directory must contain a CCF file for the first domain from each family represented in the DCF file. A matrix of 3D:1D scores (environment:residue scoring matrix), reflecting the probability of the amino acids occuring in different tertiary environments, is calculated from the CCF files of the first domain from each family only. The path of the CCF files is specified by the user and the file extensions is specified in the ACD file. Two log files of informative messages are also written.

## 3.0 INPUT FILE FORMAT

The format of domain CCF files is described in the DOMAINER documentation.
The format of the DCF file (domain classification file) is described in the SCOPPARSE documentation and the CATHPARSE documentation.

### Input files for usage example

### File: ../scopparse-signature/all.scop

    ID   D1CS4A_
    XX
    EN   1CS4
    XX
    TY   SCOP
    XX
    SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
    XX
    CL   Alpha and beta proteins (a+b)
    XX
    FO   Ferredoxin-like
    XX
    SF   Adenylyl and guanylyl cyclase catalytic domain
    XX
    FA   Adenylyl and guanylyl cyclase catalytic domain
    XX
    DO   Adenylyl cyclase VC1, domain C1a
    XX
    OS   Dog (Canis familiaris)
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   A CHAIN; . START; . END;
    //
    ID   D1II7A_
    XX
    EN   1II7
    XX
    TY   SCOP
    XX
    SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
    XX
    CL   Alpha and beta proteins (a+b)
    XX
    FO   Metallo-dependent phosphatases
    XX
    SF   Metallo-dependent phosphatases
    XX
    FA   DNA double-strand break repair nuclease
    XX
    DO   Mre11
    XX
    OS   Archaeon Pyrococcus furiosus
    XX
    NC   1
    XX
    CN   [1]
    XX
    CH   A CHAIN; . START; . END;
    //

## 4.0 OUTPUT FILE FORMAT

The matrix of 3D:1D scores (environment:residue scoring matrix, Figure 1) follows the standard EMBOSS format. Single letter amino acid codes are column labels and environments are row labels. The environment labels are strings of 2 characters, beginning with AA, AB, AC, through to AZ, BA, BB etc. The final row and column have the label '*' and give default substitution values (the minimum from the entire matrix). In the example shown (Figure 1), only two environments AA through AX are defined but only AA to AB are given scores owing to the sparse input data for this example (typically, all environments would receive scores).

### Output files for usage example

### File: matgen3d.calc

    SUMiNijArr
    A	0
    B	0
    C	0
    D	10
    E	0
    F	4
    G	5
    H	0
    I	5
    J	6
    K	0
    L	6
    M	12
    N	0
    O	6
    P	14
    Q	0
    R	8
    S	4
    T	0
    U	9

    NiArr
    A	10
    B	0
    C	3
    D	6
    E	11
    F	7
    G	4
    H	3
    I	7
    J	0
    K	4
    L	11
    M	1
    N	4
    O	0
    P	1
    Q	5
    R	3
    S	2
    T	3
    U	0
    V	3
    W	0
    X	0
    Y	1

      [Part of this file has been deleted for brevity]

    B	0.000

    C	0.034

    D	0.067

    E	0.124

    F	0.079

    G	0.045

    H	0.034

    I	0.079

    J	0.000

    K	0.045

    L	0.124

    M	0.011

    N	0.045

    O	0.000

    P	0.011

    Q	0.056

    R	0.034

    S	0.022

    T	0.034

    U	0.000

    V	0.034

    W	0.000

    X	0.000

    Y	0.011

    Z	0.000

### File: matgen3d.log

    D1CS4A_

    R:D-2 S:C A:63.80
    	OEnv AO:D
    R:I-3 S:T A:28.30
    	OEnv AF:I
    R:E-4 S:T A:113.00
    	OEnv AU:E
    R:G-5 S:T A:104.20
    	OEnv AU:G
    R:F-6 S:H A:23.70
    	OEnv AD:F
    R:T-7 S:H A:111.60
    	OEnv AS:T
    R:S-8 S:H A:84.60
    	OEnv AP:S
    R:L-9 S:H A:57.60
    	OEnv AJ:L
    R:A-10 S:H A:24.00
    	OEnv AD:A
    R:S-11 S:T A:78.20
    	OEnv AR:S
    R:Q-12 S:T A:78.00
    	OEnv AR:Q
    R:C-13 S:T A:28.80
    	OEnv AF:C
    R:T-14 S:C A:72.00
    	OEnv AO:T
    R:A-15 S:H A:103.00
    	OEnv AS:A
    R:Q-16 S:H A:88.10
    	OEnv AP:Q
    R:E-17 S:H A:66.30
    	OEnv AM:E
    R:L-18 S:H A:17.70
    	OEnv AD:L
    R:V-19 S:H A:79.50
    	OEnv AP:V
    R:M-20 S:H A:78.40
    	OEnv AP:M
    R:T-21 S:H A:74.90
    	OEnv AM:T
    R:L-22 S:H A:16.50
    	OEnv AD:L
    R:N-23 S:H A:94.00
    	OEnv AS:N
    R:E-24 S:H A:74.00
    	OEnv AM:E
    R:L-25 S:H A:40.60
    	OEnv AG:L

      [Part of this file has been deleted for brevity]

    	OEnv AD:F
    R:A-26 S:H A:59.60
    	OEnv AJ:A
    R:E-27 S:H A:62.30
    	OEnv AM:E
    R:A-28 S:H A:76.30
    	OEnv AP:A
    R:F-29 S:H A:20.30
    	OEnv AD:F
    R:K-30 S:H A:64.60
    	OEnv AM:K
    R:N-31 S:H A:68.30
    	OEnv AM:N
    R:A-32 S:H A:71.80
    	OEnv AM:A
    R:L-33 S:H A:42.20
    	OEnv AG:L
    R:E-34 S:H A:56.50
    	OEnv AJ:E
    R:I-35 S:H A:70.20
    	OEnv AM:I
    R:A-36 S:H A:27.70
    	OEnv AD:A
    R:V-37 S:H A:89.80
    	OEnv AP:V
    R:Q-38 S:H A:80.20
    	OEnv AP:Q
    R:E-39 S:H A:73.50
    	OEnv AM:E
    R:N-40 S:C A:109.90
    	OEnv AU:N
    R:V-41 S:C A:44.50
    	OEnv AI:V
    R:D-42 S:C A:105.60
    	OEnv AU:D
    R:F-43 S:C A:83.50
    	OEnv AR:F
    R:I-44 S:C A:43.50
    	OEnv AI:I
    R:L-45 S:C A:87.00
    	OEnv AR:L
    R:I-46 S:C A:30.40
    	OEnv AI:I
    R:A-47 S:C A:108.40
    	OEnv AU:A
    R:G-48 S:C A:102.60
    	OEnv AU:G
    R:D-49 S:C A:72.50
    	OEnv AO:D
    R:L-50 S:C A:55.40
    	OEnv AL:L

### File: matgen3d.out

    # 3D-1D Scoring matrix created by matgen3d
    # ajResidueEnv1
    # Total SCOP entries: 2
    # No. of files opened: 2
    # No. of files not opened: 0
             A     R     N     D     C     Q     E     G     H     I     L     K     M     F     P     S     T     W     Y     V     B     Z     X     *
    AA    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  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -2.64
    AB    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  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -2.64
    AC    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  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -2.64
    AD    0.98  1.09  0.80  0.39  1.09  0.58 -0.21  0.80  1.09  0.24  0.48  0.80  2.19  1.63  2.19  1.49  1.09 -2.30  2.19  1.09 -2.30 -2.30 -2.30 -2.64
    AE    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  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -2.64
    AF    0.80  2.00  1.72  1.31  2.00  1.49  0.70  1.72  2.00  1.85  0.70  1.72  3.10  1.16  3.10  2.41  2.00 -1.39  3.10  2.00 -1.39 -1.39 -1.39 -2.64
    AG    0.58  1.78  1.49  1.09  1.78  1.27  0.48  1.49  1.78  0.93  1.17  1.49  2.88  0.93  2.88  2.19  1.78 -1.61  2.88  1.78 -1.61 -1.61 -1.61 -2.64
    AH    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  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -2.64
    AI    0.58  1.78  1.49  1.09  1.78  1.27  0.48  1.49  1.78  2.03  0.48  1.49  2.88  0.93  2.88  2.19  1.78 -1.61  2.88  1.78 -1.61 -1.61 -1.61 -2.64
    AJ    1.09  1.60  1.31  0.91  1.60  1.09  0.99  1.31  1.60  0.75  0.30  1.31  2.70  0.75  2.70  2.00  1.60 -1.79  2.70  1.60 -1.79 -1.79 -1.79 -2.64
    AK    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  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -2.64
    AL    0.39  1.60  1.31  0.91  1.60  1.09  0.30  1.31  1.60  0.75  0.30  1.31  2.70  0.75  2.70  2.00  1.60 -1.79  2.70  1.60 -1.79 -1.79 -1.79 -2.64
    AM   -0.30  0.91  0.62  0.21  0.91  0.39  0.99  0.62  0.91  0.06 -0.39  0.62  2.00  0.06  2.00  1.31  0.91 -2.48  2.00  0.91 -2.48 -2.48 -2.48 -2.64
    AN    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  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -2.64
    AO    0.39  1.60  1.31  1.60  1.60  1.09  0.30  1.31  1.60  0.75  0.30  1.31  2.70  0.75  2.70  2.00  1.60 -1.79  2.70  1.60 -1.79 -1.79 -1.79 -2.64
    AP    0.24  0.75  0.46  0.06  0.75  1.34  0.14  0.46  0.75 -0.10 -0.55  0.46  1.85 -0.10  1.85  1.16  0.75 -2.64  1.85  1.44 -2.64 -2.64 -2.64 -2.64
    AQ    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  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -2.64
    AR    0.11  1.31  1.02  0.62  1.31  0.80  0.01  1.02  1.31  0.46  0.01  1.02  2.41  0.46  2.41  1.72  1.31 -2.08  2.41  1.31 -2.08 -2.08 -2.08 -2.64
    AS    0.80  2.00  1.72  1.31  2.00  1.49  0.70  1.72  2.00  1.16  0.70  1.72  3.10  1.16  3.10  2.41  2.00 -1.39  3.10  2.00 -1.39 -1.39 -1.39 -2.64
    AT    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  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 -2.64
    AU   -0.01  1.19  0.91  0.50  1.19  0.68 -0.11  2.00  1.19  0.35 -0.11  0.91  2.29  0.35  2.29  1.60  1.19 -2.20  2.29  1.19 -2.20 -2.20 -2.20 -2.64
    *    -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64 -2.64

## 5.0 DATA FILES

MATGEN3D does not use any data files.

## 6.0 USAGE

### 6.1 COMMAND LINE ARGUMENTS

    Generate a 3D-1D scoring matrix from CCF files.
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers (* if not always prompted):
       -modeposition       menu       [1] This option specifies the amino acid
                                      residue positions to use in calculating the
                                      substitution data. (Values: 1 (All amino
                                      acid positions for domains in a DCF file); 2
                                      (Ligand-binding positions.))
    *  -modeligand         menu       [1] This option specifies whether to use all
                                      ligands or a specific set of ligands
                                      present in a CON file when calculating the
                                      substitution data. (Values: 1 (All ligands
                                      within a CON file); 2 (Select ligands within
                                      a CON file.))
    *  -dcfinfile          infile     This option specifies the name of DCF file
                                      (domain classification file) (input). A
                                      'domain classification file' contains
                                      classification and other data for domains
                                      from SCOP or CATH, in DCF format
                                      (EMBL-like). The files are generated by
                                      using SCOPPARSE and CATHPARSE. Domain
                                      sequence information can be added to the
                                      file by using DOMAINSEQS.
    *  -coninfile          infile     This option specifies the location of CON
                                      files (contact files) (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.
    *  -liginfile          infile     This option specifies the location of the
                                      ligand list file. This file contains a list
                                      of ligand ('heterogen') 3-character
                                      identifier codes. One id code should be
                                      given per line.
      [-ccfddir]           directory  [./] This option specifies the location of
                                      CCF files (clean coordinate files) (input)
                                      which have been processed by using PDBPLUS.
                                      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.
    *  -ccfpdir            directory  [./] This option specifies the location of
                                      CCF files (clean coordinate files) (input)
                                      which have been processed by using PDBPLUS.
                                      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.
       -modeenvir          menu       [1] This option specifies the environment
                                      definition. See matgen3d documentation for
                                      description of definitions. (Values: 1
                                      (Env1); 2 (Env2); 3 (Env3); 4 (Env4); 5
                                      (Env5); 6 (Env6); 7 (Env7); 8 (Env8); 9
                                      (Env9); 10 (Env10); 11 (Env11); 12 (Env12);
                                      13 (Env13); 14 (Env14); 15 (Env15); 16
                                      (Env16))
      [-scmatrixfile]      outfile    [matgen3d.out] Domainatrix substitution
                                      matrix output file
      [-calclogfile]       outfile    [matgen3d.calc] Domainatrix calculations log
                                      output file
      [-logfile]           outfile    [matgen3d.log] Domainatrix log output file

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

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

       "-ccfpdir" associated qualifiers
       -extension          string     Default file extension

       "-scmatrixfile" associated qualifiers
       -odirectory2        string     Output directory

       "-calclogfile" associated qualifiers
       -odirectory3        string     Output directory

       "-logfile" associated qualifiers
       -odirectory4        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
-modeposition | list | This option specifies the amino acid residue positions to use in calculating the substitution data. |
1 | (All amino acid positions for domains in a DCF file)
2 | (Ligand-binding positions.)
| 1
-modeligand | list | This option specifies whether to use all ligands or a specific set of ligands present in a CON file when calculating the substitution data. |
1 | (All ligands within a CON file)
2 | (Select ligands within a CON file.)
| 1
-dcfinfile | infile | This option specifies the name of DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. | Input file | Required
-coninfile | infile | This option specifies the location of CON files (contact files) (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. | Input file | Required
-liginfile | infile | This option specifies the location of the ligand list file. This file contains a list of ligand ('heterogen') 3-character identifier codes. One id code should be given per line. | Input file | Required
[-ccfddir] (Parameter 1) | directory | This option specifies the location of CCF files (clean coordinate files) (input) which have been processed by using PDBPLUS. 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 | ./
-ccfpdir | directory | This option specifies the location of CCF files (clean coordinate files) (input) which have been processed by using PDBPLUS. 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 | ./
-modeenvir | list | This option specifies the environment definition. See matgen3d documentation for description of definitions. |
1 | (Env1)
2 | (Env2)
3 | (Env3)
4 | (Env4)
5 | (Env5)
6 | (Env6)
7 | (Env7)
8 | (Env8)
9 | (Env9)
10 | (Env10)
11 | (Env11)
12 | (Env12)
13 | (Env13)
14 | (Env14)
15 | (Env15)
16 | (Env16)
| 1
[-scmatrixfile] (Parameter 2) | outfile | Domainatrix substitution matrix output file | Output file | matgen3d.out
[-calclogfile] (Parameter 3) | outfile | Domainatrix calculations log output file | Output file | matgen3d.calc
[-logfile] (Parameter 4) | outfile | Domainatrix log output file | Output file | matgen3d.log
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-ccfddir" associated directory qualifiers
-extension1 -extension_ccfddir | string | Default file extension | Any string | ccf
"-ccfpdir" associated directory qualifiers
-extension | string | Default file extension | Any string | ccf
"-scmatrixfile" associated outfile qualifiers
-odirectory2 -odirectory_scmatrixfile | string | Output directory | Any string |
"-calclogfile" associated outfile qualifiers
-odirectory3 -odirectory_calclogfile | string | Output directory | Any string |
"-logfile" associated outfile qualifiers
-odirectory4 -odirectory_logfile | 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 MATGEN3D is shown below. Here is a sample session with matgen3d

    % matgen3d
    Generate a 3D-1D scoring matrix from CCF files.
    DCF file amino acid positions
             1 : All amino acid positions for domains in a DCF file
             2 : Ligand-binding positions.
    This option specifies the amino acid residue positions to use in calculating the substitution data. [1]: 1
    Domain classification file (optional): ../scopparse-signature/all.scop
    Clean domain coordinates directory [./]: ../domainer-signature
    Choose environment definition.
             1 : Env1
             2 : Env2
             3 : Env3
             4 : Env4
             5 : Env5
             6 : Env6
             7 : Env7
             8 : Env8
             9 : Env9
            10 : Env10
            11 : Env11
            12 : Env12
            13 : Env13
            14 : Env14
            15 : Env15
            16 : Env16
    This option specifies the environment definition. See matgen3d documentation for description of definitions. [1]: 1
    Domainatrix substitution matrix output file [matgen3d.out]:
    Domainatrix calculations log output file [matgen3d.calc]:
    Domainatrix log output file [matgen3d.log]:

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

## 7.0 KNOWN BUGS & WARNINGS

The CCF files read must contain secondary structure and solvent accessibility data. These can be added to the file by using PDBPLUS

## 8.0 NOTES

### 8.1 GLOSSARY OF FILE TYPES

FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO
Domain classification file (for SCOP) | DCF format (EMBL-like). | Classification and other data for domains from SCOP. | SCOPPARSE | Domain sequence information can be added to the file by using DOMAINSEQS.
Domain classification file (for CATH) | DCF format (EMBL-like). | Classification and other data for domains from CATH. | CATHPARSE | Domain sequence information can be added to the file by using DOMAINSEQS.
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.

## 9.0 DESCRIPTION

MATGEN3D generates a matrix of 3D:1D scores which give the probability of finding a certain amino acid residue (1D) in a certain environment in space (3D). The environments are defined on the basis of secondary structure and solvent accessibility. The 3D:1D scores are calculated from the first domain only from each family represented in the DCF file (input). This ensures the scores are not biased to any particular family of proteins.

## 10.0 ALGORITHM

Environment definitions will be described here.

## 11.0 RELATED APPLICATIONS

## See also

Program name | Description
--- | ---
cathparse | Generate DCF file from raw CATH files
domainalign | Generate alignments (DAF file) for nodes in a DCF file
domainnr | Remove redundant domains from a DCF file
domainrep | Reorder DCF file to identify representative structures
domainseqs | Add sequence records to a DCF file
domainsse | Add secondary structure records to a DCF file
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
libgen | Generate discriminating elements from alignments
pepcoil | Predict coiled coil regions in protein sequences
rocon | Generate a hits file from comparing two DHF files
rocplot | Perform ROC analysis on hits files
scopparse | Generate DCF file from raw SCOP files
seqalign | Extend alignments (DAF file) with sequences (DHF file)
seqfraggle | Remove fragment sequences from DHF files
seqsort | Remove ambiguous classified sequences from DHF files
seqwords | Generate DHF files from keyword search of UniProt
ssematch | Search a DCF file for secondary structure matches

## 12.0 DIAGNOSTIC ERROR MESSAGES

None.

## 13.0 AUTHORS

Waqas Awan
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

## History

## Comments

    None