• Specify template with alignment: This option allows you (usually advanced users) to specify both template structure and the target-template alignment. The available file format includes 3D format and FASTA formt.

    The 3D format is similar as the standard PDB format but two more columns are added from the template sequences, e.g.

    ATOM   2001  CA  MET     1      41.116 -30.727   6.866  129 THR
ATOM   2002  CA  ALA     2      39.261 -27.408   6.496  130 ARG
ATOM   2003  CA  ALA     3      35.665 -27.370   7.726  131 THR
ATOM   2004  CA  ARG     4      32.662 -25.111   7.172  132 ARG
ATOM   2005  CA  GLY     5      29.121 -25.194   8.602  133 ARG

Column 1 -30: Atom & Residue records of query sequence.
Column 31-54: Coordinates of atoms in query copied from corresponding atoms in template.
Column 55-59: Corresponding residue number in template based on alignment
Column 60-64: Corresponding residue name in template
    The FASTA format is similar as the standard FASTA format except that the 3D structure is attached after the sequence alignemnts. e.g. 
    >query
--------------------------------------------------------------------------
------------------------------------------------------MAARGRRAEPQGREAPGPAG
GGGGGSRWAESGSGTSPESGDEEVSGAGSSPVSGGVNLFANDGSFLELFKRKMEEEQRQRQEEPPPGPQRPDQS
AAAAGPGDPKRKGGPGSTLS---------FVGKRRGGNKLALKTGIVAKKQKTEDEVL------------TSKG
DAWAKYMAEVKKYKAHQCGDDDKTRPLVK---------------------------------------------
--------------------------------------------------------------------------
>1w0r:A
DPVLCFTQYEESSGKCKGLLGGGVSVEDCCLNTAFAYQKRSGGLCQPCRSPRWSLWSTWAPCSVTCSEGSQLRY
RRCVGWNGQCSGKVAPGTLEWQLQACEDQQCCPEMGGWSGWGPWEPCSVTCSKGTRTRRRACNHPAPKCGGHCP
GQAQESEACDTQQVCPTHGAWATWGPWTPCSASCHGG--PHEPKETRSRKCSAPEPSQKPPGKPCPGLAYEQRR
CTGLPPCPVAGGWGPWGPVSPCPVTCGLGQTMEQRTCNHPVPQHGGPFCAGDATRTHICNTAVPCPVDGEWDSW
GEWSPCIRRNMKSISCQEIPGQQSRGRTCRGRKFDGHRCAGQQQDIRHCYSIQHCPLKGSWSEWSTWGLCMPPC
GPNPTRARQRLCTPLLPKYPPTVSMVEGQGEKNVTFWGRPLPRCEELQGQKLVVEEKRPCLHVPACKDPEEEEL

REMARK The following is the PDB file of 1w0r:A
ATOM      1  N   ASP     1     -61.352  10.686 -21.622
ATOM      2  CA  ASP     1     -61.577   9.382 -21.306
ATOM      3  C   ASP     1     -60.494   8.357 -21.572
ATOM      4  O   ASP     1     -59.461   8.661 -22.046
ATOM      5  CB  ASP     1     -62.869   9.947 -21.978
ATOM      6  CG  ASP     1     -64.050   9.936 -21.019
ATOM      7  OD1 ASP     1     -64.163   9.015 -20.186
ATOM      8  OD2 ASP     1     -64.907  10.837 -21.154
ATOM      9  N   PRO     2     -60.719   7.053 -21.256
...
ATOM   3368  OE2 GLU   441       3.538 -11.561 -19.634
ATOM   3369  N   LEU   442       5.760 -10.509 -22.452
ATOM   3370  CA  LEU   442       4.343 -10.088 -22.296
ATOM   3371  C   LEU   442       3.130 -10.010 -23.201
ATOM   3372  O   LEU   442       3.217  -9.645 -24.316
ATOM   3373  CB  LEU   442       2.901 -10.133 -22.751
ATOM   3374  CG  LEU   442       1.899  -9.162 -22.168
ATOM   3375  CD1 LEU   442       0.483  -9.471 -22.688
ATOM   3376  CD2 LEU   442       1.922  -9.267 -20.645
ATOM   3377  OXT LEU   442       2.654  -9.424 -25.326
END
    Note: To avoid the possible error in reproducing template structure and alignments, rather than specifying PDB ID, the users who use FASTA format must attach the original PDB structure of the template in the FASTA file, see the example.