
                          DOMAINRESO 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

   Removes low resolution domains from a DCF file (domain classification
   file)

2.0 INPUTS & OUTPUTS

   DOMAINRESO reads a DCF file and writes a DCF file containing the same
   domains excluding those whose resolution (Angstrom) of structure
   determination exceeds a user-defined threshold. The resolution data
   are taken from CCF (clean coordinate files) whose path and file
   extension (via the ACD file) are specified by the user. The names of
   the input and output files are also 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.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 format of the DCF file is described in the SCOPPARSE
   documentation.

  Output files for usage example

  File: all_2.3.scop

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;
//

5.0 DATA FILES

   DOMAINRESO does not use any data files.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers:
  [-cpdbpath]          dirlist    This option specifies the location of domain
                                  CCF file (clean coordinate files) (input).
                                  A 'clean cordinate file' contains coordinate
                                  and other data for a single PDB file or a
                                  single domain from SCOP or CATH, 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.
  [-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.
   -threshold          float      This option specifies the threshold for
                                  inclusion (Angstroms). Domains exceeding the
                                  threshold for inclusion (Angstroms) will
                                  not be given in the output file.
  [-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
   -odirectory3        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
   [-cpdbpath]
   (Parameter 1) This option specifies the location of domain CCF file
   (clean coordinate files) (input). A 'clean cordinate file' contains
   coordinate and other data for a single PDB file or a single domain
   from SCOP or CATH, 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 ./
   [-dcfinfile]
   (Parameter 2) 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
   -threshold This option specifies the threshold for inclusion
   (Angstroms). Domains exceeding the threshold for inclusion (Angstroms)
   will not be given in the output file. Any numeric value 2.8
   [-dcfoutfile]
   (Parameter 3) 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 DOMAINRESO is shown below. The DCF
   file /test_data/all.scop was read and a DCF file called
   /test_data/domainreso/all_2.3.scop was written containing only those
   domains of 2.3 Angstrom resolution or better. Resolution data were
   taken from domain coordinte files in the directory /test_data. Here is
   a sample session with domainreso


% domainreso 
Removes low resolution domains from a DCF file (domain classification
file).
Location of domain CCF file (clean coordinate files) (input). [./]: structure
Name of DCF file (domain classification file) (input).: all.scop
Threshold for inclusion (Angstroms). [2.8]: 2.3
Name of DCF file (domain classification file) (output). [test.scop]: all_2.3.sc
op

/ebi/services/idata/pmr/hgmp/test/data/structure/1cs4.ccf
/ebi/services/idata/pmr/hgmp/test/data/structure/1ii7.ccf
/ebi/services/idata/pmr/hgmp/test/data/structure/d1cs4a_.ccf
/ebi/services/idata/pmr/hgmp/test/data/structure/d1ii7a_.ccf

   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.


domainreso /test_data /test_data/all.scop /test_data/domainreso/all_2.3.scop -t
hreshold 2.3

7.0 KNOWN BUGS & WARNINGS

   No known bugs.

8.0 NOTES

   Domains that lack a value for resolution in the CCF file (e.g.
   theoretical models and NMR structures) are included in the output
   file.

  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.
   Clean coordinate file (for domain) CCF format (EMBL-like format for
   protein coordinate and derived data). Coordinate and other 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.

   None

9.0 DESCRIPTION

   It is desirable to omit poor resolution protein structures when
   performing certain analyses of protein domains. DOMAINRESO reads a DCF
   file (domain classification file) and writes one containing the same
   domains excluding those whose resolution (Angstrom) of structure
   determination exceeds a user-defined threshold.

10.0 ALGORITHM

   None.

11.0 RELATED APPLICATIONS

See also

   Program name Description
   contactcount Counts specific versus non-specific contacts in a
   directory of cleaned protein chain contact files
   contacts Reads CCF files (clean coordinate files) and writes CON files
   (contact files) of intra-chain residue-residue contact data
   domainalign Generates DAF files (domain alignment files) of
   structure-based sequence alignments for nodes in a DCF file (domain
   classification file)
   domainrep Reorder DCF file (domain classification file) so that the
   representative structure of each user-specified node is given first
   interface Reads CCF files (clean coordinate files) and writes CON
   files (contact files) of inter-chain residue-residue contact data
   libgen Generates various types of discriminating elements for each
   alignment in a directory
   psiphi Calculates phi and psi torsion angles from cleaned EMBOSS-style
   protein co-ordinate file
   rocon Reads a DHF file (domain hits file) of hits (sequences of
   unknown structural classification) and a DHF file of validation
   sequences (known classification) and writes a 'hits file' for the
   hits, which are classified and rank-ordered on the basis of score
   rocplot Provides interpretation and graphical display of the
   performance of discriminating elements (e.g. profiles for protein
   families). rocplot reads file(s) of hits from discriminator-database
   search(es), performs ROC analysis on the hits, and writes graphs
   illustrating the diagnostic performance of the discriminating elements
   seqalign Reads a DAF file (domain alignment file) and a DHF file
   (domain hits file) and writes a DAF file extended with the hits
   seqfraggle Removes fragments from DHF files (domain hits files) or
   other files of sequences
   seqsearch Generate database hits (sequences) for nodes in a DCF file
   (domain classification file) by using PSI-BLAST
   seqsort Reads DHF files (domain hits files) of database hits
   (sequences) and removes hits of ambiguous classification
   seqwords Generates DHF files (domain hits files) of database hits
   (sequences) for nodes in a DCF file (domain classification file) by
   keyword search of UniProt
   siggen Generates a sparse protein signature from an alignment and
   residue contact data
   sigscan Generates a DHF file (domain hits file) of hits (sequences)
   from scanning a signature against a sequence database

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
