Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-3670

Import alignment of structures from ChimeraX matchmaker

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.2
    • Fix Version/s: None
    • Component/s: chimerax, Structures
    • Labels:
      None

      Description

      The match command in ChimeraX can report the final alignment when the "verbose true" switch is provided (see output below). Jalview could offer a 'align structures with MatchMaker' option that executes the command for selected sequences/regions, imports the resulting alignment and induces an alignment of associated sequences according to the sequence/structure mapping and the matched residues.

      matchmaker #2/A to #1/A verbose true
      Parameters
      Chain pairing bb
      Alignment algorithm Needleman-Wunsch
      Similarity matrix BLOSUM-62
      SS fraction 0.3
      Gap open (HH/SS/other) 18/18/6
      Gap extend 1
      SS matrix
      H S O
      H 6 -9 -6
      S 6 -6
      O 4
      Iteration cutoff 2

      Matchmaker 4ZHP, chain A (#1) with 1A70, chain A (#2), sequence alignment score = 401.4
      RMSD between 95 pruned atom pairs is 0.530 angstroms; (across all 97 pairs: 0.980)

      Sequences:
      4ZHP, chain A MASYKVKLITPDGPIEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDVTIETHKEEELTALEHHHHHH
      1A70, chain A .AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKKEELTA........
      Residues:
      None, 4ZHP #1/A ALA 2, 4ZHP #1/A SER 3, 4ZHP #1/A TYR 4, 4ZHP #1/A LYS 5, 4ZHP #1/A VAL 6, 4ZHP #1/A LYS 7, 4ZHP #1/A LEU 8, 4ZHP #1/A ILE 9, 4ZHP #1/A THR 10, 4ZHP #1/A PRO 11, 4ZHP #1/A ASP 12, 4ZHP #1/A GLY 13, 4ZHP #1/A PRO 14, 4ZHP #1/A ILE 15, 4ZHP #1/A GLU 16, 4ZHP #1/A PHE 17, 4ZHP #1/A GLU 18, 4ZHP #1/A CYS 19, 4ZHP #1/A PRO 20, 4ZHP #1/A ASP 21, 4ZHP #1/A ASP 22, 4ZHP #1/A VAL 23, 4ZHP #1/A TYR 24, 4ZHP #1/A ILE 25, 4ZHP #1/A LEU 26, 4ZHP #1/A ASP 27, 4ZHP #1/A GLN 28, 4ZHP #1/A ALA 29, 4ZHP #1/A GLU 30, 4ZHP #1/A GLU 31, 4ZHP #1/A GLU 32, 4ZHP #1/A GLY 33, 4ZHP #1/A HIS 34, 4ZHP #1/A ASP 35, 4ZHP #1/A LEU 36, 4ZHP #1/A PRO 37, 4ZHP #1/A TYR 38, 4ZHP #1/A SER 39, 4ZHP #1/A CYS 40, 4ZHP #1/A ARG 41, 4ZHP #1/A ALA 42, 4ZHP #1/A GLY 43, 4ZHP #1/A SER 44, 4ZHP #1/A CYS 45, 4ZHP #1/A SER 46, 4ZHP #1/A SER 47, 4ZHP #1/A CYS 48, 4ZHP #1/A ALA 49, 4ZHP #1/A GLY 50, 4ZHP #1/A LYS 51, 4ZHP #1/A VAL 52, 4ZHP #1/A THR 53, 4ZHP #1/A ALA 54, 4ZHP #1/A GLY 55, 4ZHP #1/A THR 56, 4ZHP #1/A VAL 57, 4ZHP #1/A ASP 58, 4ZHP #1/A GLN 59, 4ZHP #1/A SER 60, 4ZHP #1/A ASP 61, 4ZHP #1/A GLY 62, 4ZHP #1/A LYS 63, 4ZHP #1/A PHE 64, 4ZHP #1/A LEU 65, 4ZHP #1/A ASP 66, 4ZHP #1/A ASP 67, 4ZHP #1/A ASP 68, 4ZHP #1/A GLN 69, 4ZHP #1/A GLU 70, 4ZHP #1/A ALA 71, 4ZHP #1/A ALA 72, 4ZHP #1/A GLY 73, 4ZHP #1/A PHE 74, 4ZHP #1/A VAL 75, 4ZHP #1/A LEU 76, 4ZHP #1/A THR 77, 4ZHP #1/A CYS 78, 4ZHP #1/A VAL 79, 4ZHP #1/A ALA 80, 4ZHP #1/A TYR 81, 4ZHP #1/A PRO 82, 4ZHP #1/A LYS 83, 4ZHP #1/A CYS 84, 4ZHP #1/A ASP 85, 4ZHP #1/A VAL 86, 4ZHP #1/A THR 87, 4ZHP #1/A ILE 88, 4ZHP #1/A GLU 89, 4ZHP #1/A THR 90, 4ZHP #1/A HIS 91, 4ZHP #1/A LYS 92, 4ZHP #1/A GLU 93, 4ZHP #1/A GLU 94, 4ZHP #1/A GLU 95, 4ZHP #1/A LEU 96, 4ZHP #1/A THR 97, 4ZHP #1/A ALA 98, 4ZHP #1/A LEU 99, None, None, None, None, None, None, None
      1A70 #2/A ALA 1, 1A70 #2/A ALA 2, 1A70 #2/A TYR 3, 1A70 #2/A LYS 4, 1A70 #2/A VAL 5, 1A70 #2/A THR 6, 1A70 #2/A LEU 7, 1A70 #2/A VAL 8, 1A70 #2/A THR 9, 1A70 #2/A PRO 10, 1A70 #2/A THR 11, 1A70 #2/A GLY 12, 1A70 #2/A ASN 13, 1A70 #2/A VAL 14, 1A70 #2/A GLU 15, 1A70 #2/A PHE 16, 1A70 #2/A GLN 17, 1A70 #2/A CYS 18, 1A70 #2/A PRO 19, 1A70 #2/A ASP 20, 1A70 #2/A ASP 21, 1A70 #2/A VAL 22, 1A70 #2/A TYR 23, 1A70 #2/A ILE 24, 1A70 #2/A LEU 25, 1A70 #2/A ASP 26, 1A70 #2/A ALA 27, 1A70 #2/A ALA 28, 1A70 #2/A GLU 29, 1A70 #2/A GLU 30, 1A70 #2/A GLU 31, 1A70 #2/A GLY 32, 1A70 #2/A ILE 33, 1A70 #2/A ASP 34, 1A70 #2/A LEU 35, 1A70 #2/A PRO 36, 1A70 #2/A TYR 37, 1A70 #2/A SER 38, 1A70 #2/A CYS 39, 1A70 #2/A ARG 40, 1A70 #2/A ALA 41, 1A70 #2/A GLY 42, 1A70 #2/A SER 43, 1A70 #2/A CYS 44, 1A70 #2/A SER 45, 1A70 #2/A SER 46, 1A70 #2/A CYS 47, 1A70 #2/A ALA 48, 1A70 #2/A GLY 49, 1A70 #2/A LYS 50, 1A70 #2/A LEU 51, 1A70 #2/A LYS 52, 1A70 #2/A THR 53, 1A70 #2/A GLY 54, 1A70 #2/A SER 55, 1A70 #2/A LEU 56, 1A70 #2/A ASN 57, 1A70 #2/A GLN 58, 1A70 #2/A ASP 59, 1A70 #2/A ASP 60, 1A70 #2/A GLN 61, 1A70 #2/A SER 62, 1A70 #2/A PHE 63, 1A70 #2/A LEU 64, 1A70 #2/A ASP 65, 1A70 #2/A ASP 66, 1A70 #2/A ASP 67, 1A70 #2/A GLN 68, 1A70 #2/A ILE 69, 1A70 #2/A ASP 70, 1A70 #2/A GLU 71, 1A70 #2/A GLY 72, 1A70 #2/A TRP 73, 1A70 #2/A VAL 74, 1A70 #2/A LEU 75, 1A70 #2/A THR 76, 1A70 #2/A CYS 77, 1A70 #2/A ALA 78, 1A70 #2/A ALA 79, 1A70 #2/A TYR 80, 1A70 #2/A PRO 81, 1A70 #2/A VAL 82, 1A70 #2/A SER 83, 1A70 #2/A ASP 84, 1A70 #2/A VAL 85, 1A70 #2/A THR 86, 1A70 #2/A ILE 87, 1A70 #2/A GLU 88, 1A70 #2/A THR 89, 1A70 #2/A HIS 90, 1A70 #2/A LYS 91, 1A70 #2/A LYS 92, 1A70 #2/A GLU 93, 1A70 #2/A GLU 94, 1A70 #2/A LEU 95, 1A70 #2/A THR 96, 1A70 #2/A ALA 97
      Residue usage in match (1=used, 0=unused):
      0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
      1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0

        Attachments

          Activity

            People

            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
            Votes:
            0 Vote for this issue
            Watchers:
            1 Start watching this issue

              Dates

              Created:
              Updated: