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  1. UGENE
  2. UGENE-4912

Incorrect loading of chain identifiers from PDB files

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    Details

    • Story Points:
      5
    • Tests Type:
      GUI automatic
    • Sprint:
      DEV-02/12/2015
    • Affect Type:
      Userdefined

      Description


      The issue must be fixed and tested until Nov. 18!!

      In the current UGENE version names of chains, loaded from a PDB file, are numerical. This is incorrect. The names are available in the PDB format and must be used in the UGENE GUI - use chain identifier field from the "ATOM" records.

      For details see the use cases below, the attached screenshots, and the format specification:
      http://www.wwpdb.org/docs/documentation/file-format/PDB_format_1996.pdf (p.174 - the chapter about "ATOM")

      Use case 1:

      1. Open a PDB file with several "MOLECULE" records (e.g. 1FDL).
        Expected state: The correct chain names are shown in the Project View and in each single-sequence view of the Sequence View.
      2. Open an annotation node in the Annotations Editor to see its qualifiers.
        Expected state: There is "molecule_name" filed. It has a correct molecule name, read from the PDB file header, NOT the chain name.
      3. Select "Structural Alignment > Align With" item in the context menu.
        Expected state:
        • The correct chain names are available in the "Chain" menu.

      Use case 2:
      The same as UC1, but use a PDB file with molecules that have several chains, i.e. the comma-separated list of chain identifiers (e.g. 3INS).

        Attachments

        1. 1FDL_text_chains.png
          1FDL_text_chains.png
          9 kB
        2. 1FDL.png
          1FDL.png
          13 kB
        3. 3INS_chain_ids.png
          3INS_chain_ids.png
          14 kB
        4. 3INS_text_chains.png
          3INS_text_chains.png
          14 kB
        5. chain_id_and_qualifiers.jpg
          chain_id_and_qualifiers.jpg
          11 kB
        6. project_view_chains.png
          project_view_chains.png
          15 kB
        7. sequence_views_chains.png
          sequence_views_chains.png
          14 kB
        8. structural_alignment_chains.png
          structural_alignment_chains.png
          23 kB

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              People

              Assignee:
              artyom_s Artyom Savchenko
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Denis Kandrov
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: