
                          DOMAINREP 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

   Reorder DCF file to identify representative structures

2.0 INPUTS & OUTPUTS

   DOMAINREP reads a DCF file (domain classification file) and writes a
   DCF file containing the same data except that the order of domains
   within each user-specified node (e.g. family) in the hierarchy may be
   changed so that the representative structure of each node is given
   first. The representative structure is found by using stamp and this
   application must be installed on the system that is running DOMAINREP
   and correctly configured (see 'Notes' below). A 'domain PDB file' for
   each domain in the DCF file must exist in a directory specified in the
   stamp "pdb.directories" file (see 'Notes' below). The domain PDB file
   contains coordinate data for a single domain from SCOP or CATH, in PDB
   format. The input and output files are specified by the user.

3.0 INPUT FILE FORMAT

   The format of the DCF file is described in the SCOPPARSE
   documentation.

  Input files for usage example

  File: all.scop2

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   D1FX2A_
XX
EN   1FX2
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 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   Receptor-type monomeric adenylyl cyclase
XX
OS   Trypanosome (Trypanosoma brucei), different isoform
XX
NC   1
XX
CN   [1]
XX


  [Part of this file has been deleted for brevity]

XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   B CHAIN; 8 START; 100 END;
//
ID   D4AT1D1
XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   D CHAIN; 8 START; 100 END;
//

4.0 OUTPUT FILE FORMAT

   The format of the DCF file is described in the SCOPPARSE
   documentation.

  Output files for usage example

  File: all_rep1st.scop

ID   D4AT1B1
XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   B CHAIN; 8 START; 100 END;
//
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


  [Part of this file has been deleted for brevity]

XX
EN   1FX2
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 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   Receptor-type monomeric adenylyl cyclase
XX
OS   Trypanosome (Trypanosoma brucei), different isoform
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D4AT1D1
XX
EN   4AT1
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO   Aspartate carbamoyltransferase
XX
OS   Escherichia coli
XX
NC   1
XX
CN   [1]
XX
CH   D CHAIN; 8 START; 100 END;
//

5.0 DATA FILES

   DOMAINREP does not use any data files but does make use of the stamp
   "pdb.directories" file (see 'Notes').

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers:
  [-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.
   -node               menu       This option specifies the node fore
                                  reordering the file. Reordering can be done
                                  for any specified node in the SCOP or CATH
                                  hierarchies. For example by selecting
                                  'Class' entries belonging to the same Class
                                  will be reordered in turn.
  [-dcfoutfile]        outfile    This option specifies the name of DCF file
                                  (domain classification file) (output). 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.

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

   "-dcfoutfile" associated qualifiers
   -odirectory2        string     Output directory

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


   Standard (Mandatory) qualifiers Allowed values Default
   [-dcfinfile]
   (Parameter 1) 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
   -node This option specifies the node fore reordering the file.
   Reordering can be done for any specified node in the SCOP or CATH
   hierarchies. For example by selecting 'Class' entries belonging to the
   same Class will be reordered in turn.
   1 (Class (SCOP))
   2 (Fold (SCOP))
   3 (Superfamily (SCOP))
   4 (Family (SCOP))
   5 (Class (CATH))
   6 (Architecture (CATH))
   7 (Topology (CATH))
   8 (Homologous Superfamily (CATH))
   9 (Family (CATH))
   1
   [-dcfoutfile]
   (Parameter 2) This option specifies the name of DCF file (domain
   classification file) (output). 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. Output file test.scop
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

  6.2 EXAMPLE SESSION

   An example of interactive use of DOMAINREP is shown below. Here is a
   sample session with domainrep


% domainrep 
Reorder DCF file to identify representative structures.
Name of DCF file (domain classification file) (input).: all.scop2
Node at which to reorder file
         1 : Class (SCOP)
         2 : Fold (SCOP)
         3 : Superfamily (SCOP)
         4 : Family (SCOP)
         5 : Class (CATH)
         6 : Architecture (CATH)
         7 : Topology (CATH)
         8 : Homologous Superfamily (CATH)
         9 : Family (CATH)
Select number. [1]: 2
Name of DCF file (domain classification file) (output). [test.scop]: all_rep1st
.scop

stamp -l ./domainrep-1121336717.25929.dom -s -n 2 -slide 5 -prefix ./domainrep-
1121336717.25929 -d ./domainrep-1121336717.25929.set > ./domainrep-1121336717.2
5929.out

stamp -l ./domainrep-1121336717.25929.dom -s -n 2 -slide 5 -prefix ./domainrep-
1121336717.25929 -d ./domainrep-1121336717.25929.set > ./domainrep-1121336717.2
5929.out

stamp -l ./domainrep-1121336717.25929.dom -s -n 2 -slide 5 -prefix ./domainrep-
1121336717.25929 -d ./domainrep-1121336717.25929.set > ./domainrep-1121336717.2
5929.out

stamp -l ./domainrep-1121336717.25929.dom -s -n 2 -slide 5 -prefix ./domainrep-
1121336717.25929 -d ./domainrep-1121336717.25929.set > ./domainrep-1121336717.2
5929.out

stamp -l ./domainrep-1121336717.25929.dom -s -n 2 -slide 5 -prefix ./domainrep-
1121336717.25929 -d ./domainrep-1121336717.25929.set > ./domainrep-1121336717.2
5929.out

stamp -l ./domainrep-1121336717.25929.dom -s -n 2 -slide 5 -prefix ./domainrep-
1121336717.25929 -d ./domainrep-1121336717.25929.set > ./domainrep-1121336717.2
5929.out


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

   The following command line would achieve the same result.


domainrep test_data/all.scop test_data/domainrep/all_rep1st.scop -node 4

7.0 KNOWN BUGS & WARNINGS

   None.

8.0 NOTES

   stamp modification
   DOMAINREP will only run with with a version of stamp which has been
   modified so that PDB id codes of length greater than 4 characters are
   acceptable. This involves a trivial change to the stamp module
   getdomain.c (around line number 155), a 4 must be changed to a 7 as
   follows:

temp=getfile(domain[0].id,dirfile,4,OUTPUT);
< change to ... >
temp=getfile(domain[0].id,dirfile,7,OUTPUT);

   stamp configuration
   stamp searches for pdb files with a certain prefix, extension and path
   as specified in the stamp "pdb.directories" file, which should look
   like something like this (change the text according to your system
   setup):

/data/pdb - -
/data/pdb _ .ent
/data/pdb _ .pdb
/data/pdb pdb .ent
/data/pdbscop _ _
/data/pdbscop _ .ent
/data/pdbscop _ .pdb
/data/pdbscop pdb .ent
./ _ _
./ _ .ent
./ _ .ent.z
./ _ .ent.gz
./ _ .pdb
./ _ .pdb.Z
./ _ .pdb.gz
./ pdb .ent
./ pdb .ent.Z
./ pdb .ent.gz
/data/CASS1/pdb/coords/ _ .pdb
/data/CASS1/pdb/coords/ _ .pdb.Z
/data/CASS1/pdb/coords/ _ .pdb.gz

   RFCGR Users
   For users of the RFCGR computer systems, the modified stamp code is
   kept in /packages/stamp/src2. When running DOMAINREP at the RFCGR it
   is essential that the command 'use stamp2' (which runs the script
   /packages/menu/USE/stamp2) is given before DOMAINREP is run. This will
   ensure that the modified version of stamp is used. For RFCGR users,
   the pdb.directories file is /packages/stamp/defs/pdb.directories.
   Domain PDB files (pdb format) for SCOP domains are stored in
   /data/pdbscop. None

  8.1 GLOSSARY OF FILE TYPES

   FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
   Domain classification file (for SCOP) DCF format (EMBL-like format for
   domain classification data). 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 format for
   domain classification data). Classification and other data for domains
   from CATH. CATHPARSE Domain sequence information can be added to the
   file by using DOMAINSEQS.
   Domain PDB file PDB format for domain coordinate data. Coordinate data
   for a single domain from SCOP or CATH. DOMAINER N.A.

9.0 DESCRIPTION

   The protein structural alignment program stamp aligns multiple
   structures to a seed structure. The best alignments will result when
   the seed is the best available representative of the entire set, i.e.
   in structural terms, is more similar to the other structures than any
   other structure.
   DOMAINALIGN calls stamp to generate alignments of domains belonging to
   the same node (e.g. family) in a DCF file. DOMAINALIGN will produce
   better alignments if the DCF file is reordered so that the
   representative structure of each node is given first, because the
   first strucutres are used as the seeds. The reordering of the DCF file
   is done by using DOMAINREP.

10.0 ALGORITHM

   More information on stamp can be found at
   http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/

11.0 RELATED APPLICATIONS

See also

   Program name                       Description
   contactcount Count specific versus non-specific contacts
   contacts     Generate intra-chain CON files from CCF files
   domainalign  Generate alignments (DAF file) for nodes in a DCF file
   domainreso   Remove low resolution domains from a DCF file
   interface    Generate inter-chain CON files from CCF files
   libgen       Generate discriminating elements from alignments
   matgen3d     Generate a 3D-1D scoring matrix from CCF files
   psiphi       Phi and psi torsion angles from protein coordinates
   rocon        Generates a hits file from comparing two DHF files
   rocplot      Performs ROC analysis on hits files
   scorecmapdir Contact scores for cleaned protein chain contact files
   seqalign     Extend alignments (DAF file) with sequences (DHF file)
   seqfraggle   Removes fragment sequences from DHF files
   seqsearch    Generate PSI-BLAST hits (DHF file) from a DAF file
   seqsort      Remove ambiguous classified sequences from DHF files
   seqwords     Generates DHF files from keyword search of UniProt
   siggen       Generates a sparse protein signature from an alignment
   siggenlig    Generate ligand-binding signatures from a CON file
   sigscan      Generate hits (DHF file) from a signature search
   sigscanlig   Search ligand-signature library & write hits (LHF file)

12.0 DIAGNOSTIC ERROR MESSAGES

   None.

13.0 AUTHORS

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

14.0 REFERENCES

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

  14.1 Other useful references
