• Specify template with alignment: This option allows you (usually advanced users) to specify both template structure and the target-template alignment. You can use either 3D Format or FASTA Format.

    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.
    >TARGET
    --------------------------------------------------------------------------
    ------------------------------------------------------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:
    (a) 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.
    (b) The query name specified in the FASTA alignment (in the above example as "TARGET") should be the same as the name specified in ID form on the submission page. If you leave the ID form blank, the description line of query in the FASTA alignment should be specified as ">your_protein".