                          DOMAINALIGN 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 alignments (DAF file) for nodes in a DCF file

2.0 INPUTS & OUTPUTS

   DOMAINALIGN generates a DAF file (domain alignment file) for each
   user-defined node (e.g. family or superfamily) in a DCF file (domain
   classification file) that is read. Each DAF file contains a
   structure-based sequence alignment annotated with domain classification
   data. If the STAMP algorithm is used, structural superimpositions are
   also generated and saved to file (PDB format). The alignments are
   calculated by using STAMP or TCOFFEE and these applications must be
   installed on the system that is running DOMAINALIGN (see 'Notes'
   below).
   Clearly no alignment can be generated for nodes with a single entry
   (domain) only: sequences for such domains are (optionally) written to
   file (fasta format).
   DOMAINALIGN requires a directory of domain PDB files; the path and
   extension of these must be set by the user (via the ACD file) and also
   specified in the STAMP "pdb.directories" file (see 'Notes' below)
   A log file of diagnostic messages is written. The identifier (e.g SCOP
   Sunid) of the nodes from the DCF file are used to name the output
   files. The user also specifies the input file, paths for the two types
   of alignment files (output), path of singlet sequence files (if output)
   and name of log file.

3.0 INPUT FILE FORMAT

   The format of the DCF (domain classification file) is described in
   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

   Structure-based sequence alignment
   The DAF (domain alignment file) format (Figure 1) consists of an
   alignment in EMBOSS "simple" multiple sequence alignment format with
   domain classification records. All lines other than sequence lines
   begin with '#' to denote a comment. The domain classification records
   for the appopriate node from the DCF file are given at the top of the
   file above the alignment. The records shown are TY (domain type, either
   SCOP or CATH), CL (class), FO (fold), SF (superfamily) and FA (family).
   For CATH domains, AR (architecture) and TP (topology) may also be
   given. Regardless of which node (family, superfamily etc) is
   represented, a unique identifier for the node is given after SI. Below
   the classification records, there are blocks that contain the sequence
   names, positions and aligned sequences. The names are the 7 character
   domain identifier codes taken from the DCF file. The positions are the
   start and end residue positions of the appropriate section of sequence.
   The sequence uses '-' as a gap character. The STAMP 'Post similar' line
   is given as a markup line underneath the sequence but no dssp
   assignments are written.

  Output files for usage example

  File: 54894.ent

REMARK Output from transform
REMARK  STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992)
REMARK Domains were read from the file ./domainalign-1234567890.1234.sort
REMARK Chains are labelled sequentially starting with 'A' and
REMARK  after the order given in the file ./domainalign-1234567890.1234.sort
REMARK The domains in this file are:
REMARK       d4at1b1  chain A
REMARK       d4at1d1_1  chain B
REMARK Does not include heteroatoms
REMARK  Does not include DNA/RNA
REMARK Does not include waters
ATOM      1  N   GLY A   8      13.557  82.383  35.829  1.00 92.06           N
ATOM      2  CA  GLY A   8      14.363  82.355  34.620  1.00 92.63           C
ATOM      3  C   GLY A   8      14.480  83.797  34.150  1.00 91.80           C
ATOM      4  O   GLY A   8      13.625  84.596  34.527  1.00 93.34           O
ATOM      5  N   VAL A   9      15.499  84.132  33.352  1.00 90.04           N
ATOM      6  CA  VAL A   9      15.799  85.525  33.008  1.00 89.55           C
ATOM      7  C   VAL A   9      15.294  86.094  31.646  1.00 90.94           C
ATOM      8  O   VAL A   9      14.395  85.528  31.008  1.00 91.46           O
ATOM      9  CB  VAL A   9      17.381  85.731  33.167  1.00 88.13           C
ATOM     10  CG1 VAL A   9      17.571  86.421  34.506  1.00 86.27           C
ATOM     11  CG2 VAL A   9      18.232  84.456  33.191  1.00 86.95           C
ATOM     12  N   GLU A  10      15.892  87.223  31.201  1.00 89.98           N
ATOM     13  CA  GLU A  10      15.543  87.988  30.004  1.00 87.19           C
ATOM     14  C   GLU A  10      16.748  88.251  29.055  1.00 83.25           C
ATOM     15  O   GLU A  10      17.879  87.817  29.318  1.00 81.89           O
ATOM     16  CB  GLU A  10      14.876  89.324  30.474  1.00 89.77           C
ATOM     17  CG  GLU A  10      15.390  90.058  31.748  1.00 93.53           C
ATOM     18  CD  GLU A  10      16.862  90.513  31.791  1.00 96.84           C
ATOM     19  OE1 GLU A  10      17.570  90.129  32.731  1.00 98.75           O
ATOM     20  OE2 GLU A  10      17.306  91.258  30.905  1.00 97.00           O
ATOM     21  N   ALA A  11      16.471  89.023  27.987  1.00 77.76           N
ATOM     22  CA  ALA A  11      17.315  89.379  26.829  1.00 71.32           C
ATOM     23  C   ALA A  11      18.829  89.525  26.622  1.00 65.96           C
ATOM     24  O   ALA A  11      19.605  90.124  27.370  1.00 64.35           O
ATOM     25  CB  ALA A  11      16.692  90.608  26.193  1.00 70.48           C
ATOM     26  N   ILE A  12      19.133  88.956  25.457  1.00 62.08           N
ATOM     27  CA  ILE A  12      20.419  88.929  24.778  1.00 60.99           C
ATOM     28  C   ILE A  12      19.984  89.116  23.325  1.00 61.87           C
ATOM     29  O   ILE A  12      18.841  88.755  22.999  1.00 62.16           O
ATOM     30  CB  ILE A  12      21.198  87.545  24.850  1.00 59.43           C
ATOM     31  CG1 ILE A  12      20.354  86.363  24.347  1.00 55.38           C
ATOM     32  CG2 ILE A  12      21.619  87.298  26.290  1.00 59.29           C
ATOM     33  CD1 ILE A  12      21.107  85.072  24.029  1.00 50.25           C
ATOM     34  N   LYS A  13      20.745  89.683  22.389  1.00 62.88           N
ATOM     35  CA  LYS A  13      20.307  89.668  20.991  1.00 63.76           C
ATOM     36  C   LYS A  13      21.229  88.611  20.439  1.00 63.26           C
ATOM     37  O   LYS A  13      22.425  88.631  20.755  1.00 63.54           O
ATOM     38  CB  LYS A  13      20.570  90.941  20.133  1.00 65.83           C
ATOM     39  CG  LYS A  13      21.100  92.232  20.765  1.00 68.73           C


  [Part of this file has been deleted for brevity]

ATOM    675  O   LYS B  94      12.694  74.659  17.436  1.00 60.00           O
ATOM    676  CB  LYS B  94      11.414  76.090  20.144  1.00 54.56           C
ATOM    677  CG  LYS B  94      10.901  77.252  20.962  1.00 56.83           C
ATOM    678  CD  LYS B  94       9.923  76.671  21.990  1.00 59.11           C
ATOM    679  CE  LYS B  94       9.043  77.717  22.641  1.00 60.10           C
ATOM    680  NZ  LYS B  94       9.890  78.702  23.259  1.00 64.17           N
ATOM    681  N   SER B  95      13.444  74.034  19.484  1.00 54.16           N
ATOM    682  CA  SER B  95      13.785  72.651  19.195  1.00 49.80           C
ATOM    683  C   SER B  95      13.767  71.904  20.531  1.00 49.50           C
ATOM    684  O   SER B  95      13.715  72.494  21.617  1.00 50.66           O
ATOM    685  CB  SER B  95      15.186  72.559  18.595  1.00 49.06           C
ATOM    686  OG  SER B  95      15.488  73.550  17.615  1.00 48.30           O
ATOM    687  N   ARG B  96      13.817  70.590  20.497  1.00 50.27           N
ATOM    688  CA  ARG B  96      13.868  69.771  21.694  1.00 49.58           C
ATOM    689  C   ARG B  96      14.839  68.647  21.295  1.00 47.31           C
ATOM    690  O   ARG B  96      15.006  68.414  20.088  1.00 44.69           O
ATOM    691  CB  ARG B  96      12.426  69.305  21.983  1.00 53.09           C
ATOM    692  CG  ARG B  96      12.197  68.404  23.200  1.00 58.05           C
ATOM    693  CD  ARG B  96      10.794  68.557  23.787  1.00 61.70           C
ATOM    694  NE  ARG B  96      10.618  69.895  24.354  1.00 66.11           N
ATOM    695  CZ  ARG B  96       9.772  70.814  23.850  1.00 69.37           C
ATOM    696  NH1 ARG B  96       9.702  72.024  24.422  1.00 71.16           N
ATOM    697  NH2 ARG B  96       8.988  70.558  22.790  1.00 70.99           N
ATOM    698  N   PRO B  97      15.591  68.002  22.198  1.00 47.31           N
ATOM    699  CA  PRO B  97      16.438  66.853  21.917  1.00 47.03           C
ATOM    700  C   PRO B  97      15.755  65.610  21.357  1.00 46.69           C
ATOM    701  O   PRO B  97      14.800  65.056  21.929  1.00 47.44           O
ATOM    702  CB  PRO B  97      17.138  66.581  23.238  1.00 48.99           C
ATOM    703  CG  PRO B  97      17.256  67.940  23.887  1.00 49.17           C
ATOM    704  CD  PRO B  97      15.868  68.473  23.559  1.00 49.45           C
ATOM    705  N   SER B  98      16.313  65.239  20.191  1.00 45.02           N
ATOM    706  CA  SER B  98      16.016  64.022  19.436  1.00 41.65           C
ATOM    707  C   SER B  98      17.197  63.101  19.711  1.00 39.46           C
ATOM    708  O   SER B  98      18.327  63.608  19.718  1.00 38.78           O
ATOM    709  CB  SER B  98      15.952  64.291  17.940  1.00 42.24           C
ATOM    710  OG  SER B  98      14.657  64.744  17.586  1.00 46.01           O
ATOM    711  N   LEU B  99      16.992  61.793  19.950  1.00 36.31           N
ATOM    712  CA  LEU B  99      18.078  60.869  20.273  1.00 33.04           C
ATOM    713  C   LEU B  99      19.004  60.692  19.051  1.00 33.65           C
ATOM    714  O   LEU B  99      18.467  60.339  17.994  1.00 35.86           O
ATOM    715  CB  LEU B  99      17.420  59.573  20.697  1.00 29.39           C
ATOM    716  CG  LEU B  99      18.126  58.649  21.690  1.00 28.47           C
ATOM    717  CD1 LEU B  99      18.261  59.352  23.048  1.00 27.24           C
ATOM    718  CD2 LEU B  99      17.332  57.342  21.817  1.00 25.66           C
ATOM    719  N   PRO B 100      20.325  60.971  19.041  1.00 33.12           N
ATOM    720  CA  PRO B 100      21.146  60.885  17.830  1.00 35.17           C
ATOM    721  C   PRO B 100      21.517  59.413  17.592  1.00 38.22           C
ATOM    722  O   PRO B 100      21.547  58.620  18.542  1.00 36.98           O
ATOM    723  CB  PRO B 100      22.317  61.776  18.143  1.00 34.28           C
ATOM    724  CG  PRO B 100      22.530  61.464  19.626  1.00 33.62           C
ATOM    725  CD  PRO B 100      21.124  61.360  20.204  1.00 31.93           C

  Directory: daf

   This directory contains output files, for example 54894.daf and
   55074.daf.

  File: daf/54894.daf

# TY   SCOP
# 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
# SI   54894
# XX
#         Number               10        20        30        40        50
d4at1b1              0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPXSGEMGRKDLIKIEN
      0
d4at1d1              0 GVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGXEMGRKDLIKIEN
      0
# Post_similar         111111111111111111111111111111111111111111-0-111111111111

#         Number        60        70        80        90
d4at1b1              0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP      0
d4at1d1              0 TFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLP      0
# Post_similar         1111111111111111111111111111111111111

  File: daf/55074.daf

# TY   SCOP
# 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
# SI   55074
# XX
#         Number               10        20        30        40        50
d1cs4a_              0 MMFHKIYIQKXHXDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENH
      0
d1fx2a_              0 XXNNNRAPXKEPTDPVTLIFTDIESSTALWAAXHPDLMPDAVAAHHRMVRSLIGRYK
      0
# Post_similar         --000000-0-0-1111111111111111111-000111111111111111111111

#         Number        60        70        80        90       100       110
d1cs4a_              0 CLRIKILGDCYYCVSGLPEARADHAHCCVEMGMDMIEAISLVREMXTXGXXXXXXXX
      0
d1fx2a_              0 CYEVKTVGDSFMIAXXXXSKXXXSPFAAVQLAQELQLCFLHXHDWGTNALDDSYREF
      0
# Post_similar         11111111111111----00---111111111111111111-000-0-0--------

#         Number          120       130       140       150       160       170
d1cs4a_              0 XXXXXXXXXXXXXXXXXXXXXXXXXXXVNVNMRVGIHSGRVHXCGVLGLRKWQFDVW
      0
d1fx2a_              0 EEQRAEGECEYTPPTAHMDPEVYSRLWNGLRVRVGIHTGLCDIRHDXEXVTKGYDYY
      0
# Post_similar         ---------------------------011111111111111-111-0-00001111

#         Number             180       190       200       210       220
d1cs4a_              0 SNDVTLANHMEAGGKAGRIHITKATLSYLNXXXGXDYEVEPGCGGERNXAYLKEHSI
      0
d1fx2a_              0 GRTPNMAARTESVANGGQVLMTHAAYMSLSAEDRKQIDVTALXGDXVALRGXVSDPV
      0
# Post_similar         111111111111111111111111111111---0-1111111-00-00-00-00111

#         Number      230       240       250
d1cs4a_              0 ETFLILXXXXXXXXXXXXXXXXXX      0
d1fx2a_              0 KMYQLNTVPSRNFAALRLDREYFD      0
# Post_similar         111111------------------

  File: 55074.ent

REMARK Output from transform
REMARK  STAMP Package (Russell and Barton Proteins, 14, 309-323, 1992)
REMARK Domains were read from the file ./domainalign-1234567890.1234.sort
REMARK Chains are labelled sequentially starting with 'A' and
REMARK  after the order given in the file ./domainalign-1234567890.1234.sort
REMARK The domains in this file are:
REMARK       d1cs4a_  chain A
REMARK       d1fx2a__1  chain B
REMARK Does not include heteroatoms
REMARK  Does not include DNA/RNA
REMARK Does not include waters
ATOM      1  N   MET A 377      28.568 -27.770  32.255  1.00 73.77           N
ATOM      2  CA  MET A 377      28.292 -26.443  32.794  1.00 72.28           C
ATOM      3  C   MET A 377      29.325 -25.377  32.396  1.00 69.48           C
ATOM      4  O   MET A 377      30.485 -25.687  32.098  1.00 67.04           O
ATOM      5  CB  MET A 377      28.075 -26.504  34.312  1.00 74.79           C
ATOM      6  CG  MET A 377      29.171 -27.205  35.092  1.00 78.73           C
ATOM      7  SD  MET A 377      28.708 -27.446  36.824  1.00 83.74           S
ATOM      8  CE  MET A 377      28.745 -25.745  37.440  1.00 81.94           C
ATOM      9  N   MET A 378      28.883 -24.120  32.395  1.00 66.44           N
ATOM     10  CA  MET A 378      29.698 -22.969  32.011  1.00 62.94           C
ATOM     11  C   MET A 378      30.928 -22.727  32.886  1.00 59.70           C
ATOM     12  O   MET A 378      32.059 -22.739  32.400  1.00 57.00           O
ATOM     13  CB  MET A 378      28.824 -21.715  31.966  1.00 64.01           C
ATOM     14  CG  MET A 378      27.551 -21.872  31.137  1.00 64.35           C
ATOM     15  SD  MET A 378      27.897 -22.219  29.403  1.00 67.83           S
ATOM     16  CE  MET A 378      27.844 -24.014  29.357  1.00 65.41           C
ATOM     17  N   PHE A 379      30.697 -22.474  34.167  1.00 56.03           N
ATOM     18  CA  PHE A 379      31.763 -22.225  35.123  1.00 53.16           C
ATOM     19  C   PHE A 379      32.157 -23.501  35.837  1.00 51.53           C
ATOM     20  O   PHE A 379      31.372 -24.440  35.914  1.00 53.09           O
ATOM     21  CB  PHE A 379      31.296 -21.227  36.186  1.00 54.14           C
ATOM     22  CG  PHE A 379      31.091 -19.832  35.671  1.00 51.13           C
ATOM     23  CD1 PHE A 379      29.927 -19.493  34.986  1.00 50.12           C
ATOM     24  CD2 PHE A 379      32.049 -18.846  35.907  1.00 49.63           C
ATOM     25  CE1 PHE A 379      29.716 -18.196  34.546  1.00 51.63           C
ATOM     26  CE2 PHE A 379      31.852 -17.545  35.474  1.00 50.16           C
ATOM     27  CZ  PHE A 379      30.682 -17.216  34.792  1.00 51.72           C
ATOM     28  N   HIS A 380      33.371 -23.529  36.372  1.00 50.09           N
ATOM     29  CA  HIS A 380      33.830 -24.687  37.120  1.00 49.62           C
ATOM     30  C   HIS A 380      33.046 -24.672  38.431  1.00 49.26           C
ATOM     31  O   HIS A 380      32.579 -23.623  38.866  1.00 50.30           O
ATOM     32  CB  HIS A 380      35.327 -24.574  37.439  1.00 52.29           C
ATOM     33  CG  HIS A 380      36.235 -24.929  36.299  1.00 53.66           C
ATOM     34  ND1 HIS A 380      36.782 -23.983  35.457  1.00 53.12           N
ATOM     35  CD2 HIS A 380      36.737 -26.122  35.898  1.00 52.37           C
ATOM     36  CE1 HIS A 380      37.581 -24.576  34.588  1.00 50.60           C
ATOM     37  NE2 HIS A 380      37.572 -25.873  34.833  1.00 52.60           N
ATOM     38  N   LYS A 381      32.879 -25.832  39.051  1.00 50.19           N
ATOM     39  CA  LYS A 381      32.167 -25.897  40.318  1.00 51.93           C


  [Part of this file has been deleted for brevity]

ATOM   1806  CG  ASP B1117      55.881   2.260  56.337  1.00 70.08           C
ATOM   1807  OD1 ASP B1117      55.414   2.017  55.197  1.00 73.38           O
ATOM   1808  OD2 ASP B1117      57.084   2.059  56.637  1.00 70.53           O
ATOM   1809  N   ARG B1118      52.764   0.077  56.474  1.00 66.61           N
ATOM   1810  CA  ARG B1118      52.481  -1.377  56.573  1.00 68.20           C
ATOM   1811  C   ARG B1118      53.212  -2.511  55.828  1.00 68.77           C
ATOM   1812  O   ARG B1118      54.421  -2.488  55.587  1.00 70.57           O
ATOM   1813  CB  ARG B1118      51.033  -1.596  56.196  1.00 71.02           C
ATOM   1814  CG  ARG B1118      49.988  -0.730  56.780  1.00 66.89           C
ATOM   1815  CD  ARG B1118      48.805  -0.985  55.855  1.00 69.79           C
ATOM   1816  NE  ARG B1118      47.548  -0.457  56.346  1.00 65.16           N
ATOM   1817  CZ  ARG B1118      47.350   0.805  56.714  1.00 67.30           C
ATOM   1818  NH1 ARG B1118      48.318   1.717  56.649  1.00 62.67           N
ATOM   1819  NH2 ARG B1118      46.198   1.137  57.253  1.00 60.83           N
ATOM   1820  N   GLU B1119      52.370  -3.490  55.468  1.00 74.62           N
ATOM   1821  CA  GLU B1119      52.576  -4.775  54.756  1.00 71.44           C
ATOM   1822  C   GLU B1119      51.216  -5.345  55.152  1.00 68.30           C
ATOM   1823  O   GLU B1119      50.787  -5.071  56.255  1.00 70.28           O
ATOM   1824  CB  GLU B1119      53.628  -5.683  55.451  1.00 72.63           C
ATOM   1825  CG  GLU B1119      53.056  -6.991  56.217  1.00 68.78           C
ATOM   1826  CD  GLU B1119      52.428  -6.728  57.622  1.00 67.37           C
ATOM   1827  OE1 GLU B1119      52.888  -5.743  58.270  1.00 63.79           O
ATOM   1828  OE2 GLU B1119      51.452  -7.444  58.067  1.00 24.30           O
ATOM   1829  N   TYR B1120      50.504  -6.074  54.309  1.00 69.56           N
ATOM   1830  CA  TYR B1120      49.237  -6.679  54.769  1.00 66.82           C
ATOM   1831  C   TYR B1120      49.096  -7.992  54.006  1.00 69.41           C
ATOM   1832  O   TYR B1120      49.547  -8.082  52.863  1.00 60.86           O
ATOM   1833  CB  TYR B1120      48.062  -5.721  54.629  1.00 64.84           C
ATOM   1834  CG  TYR B1120      46.960  -6.107  53.681  1.00 72.65           C
ATOM   1835  CD1 TYR B1120      47.056  -5.809  52.324  1.00 69.04           C
ATOM   1836  CD2 TYR B1120      45.764  -6.658  54.154  1.00 72.45           C
ATOM   1837  CE1 TYR B1120      45.996  -6.038  51.461  1.00 74.31           C
ATOM   1838  CE2 TYR B1120      44.688  -6.892  53.292  1.00 74.14           C
ATOM   1839  CZ  TYR B1120      44.815  -6.576  51.947  1.00 77.01           C
ATOM   1840  OH  TYR B1120      43.765  -6.791  51.087  1.00 73.74           O
ATOM   1841  N   PHE B1121      48.537  -9.016  54.663  1.00 67.32           N
ATOM   1842  CA  PHE B1121      48.401 -10.387  54.120  1.00 68.14           C
ATOM   1843  C   PHE B1121      48.561 -10.745  52.626  1.00 68.72           C
ATOM   1844  O   PHE B1121      49.618 -11.228  52.233  1.00 71.84           O
ATOM   1845  CB  PHE B1121      47.210 -11.123  54.717  1.00 64.05           C
ATOM   1846  CG  PHE B1121      47.408 -12.619  54.794  1.00 61.04           C
ATOM   1847  CD1 PHE B1121      48.271 -13.164  55.734  1.00 58.84           C
ATOM   1848  CD2 PHE B1121      46.737 -13.479  53.925  1.00 63.12           C
ATOM   1849  CE1 PHE B1121      48.466 -14.540  55.815  1.00 60.74           C
ATOM   1850  CE2 PHE B1121      46.925 -14.859  53.999  1.00 59.31           C
ATOM   1851  CZ  PHE B1121      47.788 -15.392  54.941  1.00 64.18           C
ATOM   1852  N   ASP B1122      47.527 -10.585  51.805  1.00 72.82           N
ATOM   1853  CA  ASP B1122      47.656 -10.920  50.374  1.00 73.64           C
ATOM   1854  C   ASP B1122      46.520 -10.365  49.515  1.00 74.17           C
ATOM   1855  O   ASP B1122      46.464 -10.761  48.332  1.00 75.01           O
ATOM   1856  CB  ASP B1122      47.790 -12.446  50.171  1.00 73.22           C

  File: domainalign.log

Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'
Replaced ' ' in STAMP alignment with 'X'

5.0 DATA FILES

   DOMAINALIGN does not use any data files but uses the STAMP
   "pdb.directories" file which specifies the permissible prefix,
   extension and path of PDB files used by STAMP. This file should look
   like :

 test_data/ - .dent
 /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


6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

Generate alignments (DAF file) for nodes in a DCF file.
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-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.
  [-pdbdir]            directory  [./] This option specifies the location of
                                  domain PDB files (input). A 'domain PDB
                                  file' contains coordinate data for a single
                                  domain from SCOP or CATH, in PDB format. The
                                  files are generated by using DOMAINER.
   -node               menu       [1] This option specifies the node for
                                  redundancy removal. Redundancy can be
                                  removed at any specified node in the SCOP or
                                  CATH hierarchies. For example by selecting
                                  'Class' entries belonging to the same Class
                                  will be non-redundant. (Values: 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)))
   -mode               menu       [1] This option specifies the alignment
                                  algorithm to use. (Values: 1 (STAMP); 2
                                  (TCOFFEE))
   -[no]keepsinglets   toggle     [Y] This option specifies whether to write
                                  sequences of singlet families to file. If
                                  you specify this option, the sequence for
                                  each singlet family are written to file
                                  (output).
  [-dafoutdir]         outdir     [./] This option specifies the location of
                                  DAF files (domain alignment files) (output).
                                  A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family. The files are
                                  in clustal format and are annotated with
                                  domain family classification information.
                                  The files generated by using SCOPALIGN will
                                  contain a structure-based sequence alignment
                                  of domains of known structure only. Such
                                  alignments can be extended with sequence
                                  relatives (of unknown structure) by using
                                  SEQALIGN.
*  -singletsoutdir     outdir     [./] This option specifies the location of
                                  DHF files (domain hits files) for singlet
                                  sequences (output). The singlets are written
                                  out as a 'domain hits file' - which
                                  contains database hits (sequences) with
                                  domain classification information, in FASTA
                                  format.
*  -superoutdir        outdir     [./] This option specifies the location of
                                  structural superimposition files (output). A
                                  file in PDB format of the structural
                                  superimposition is generated for each family
                                  if the STAMP algorithm is used.
   -logfile            outfile    [domainalign.log] This option specifies the
                                  name of log file (output). The log file
                                  contains messages about any errors arising
                                  while domainalign ran.

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

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

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

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

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

   "-logfile" 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


