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  1. Jalview
  2. JAL-732

automatically associate PDB files dragged onto an alignment with sequences that have high similarity and matching IDs

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    Details

    • Type: New Feature
    • Status: Resolved
    • Priority: Major
    • Resolution: Incomplete
    • Affects Version/s: None
    • Fix Version/s: 2.7, 2.8
    • Component/s: None
    • Labels:
      None

      Description

      many users needing sequence/structure alignment visualisation will have a number of specially prepared PDB files, and one or more alignments involving those files. It is extremely cumbersome to manually add associations between specific files and sequences in the alignment. One way this mapping could be automated is to allow the user to drag a set of files (or a directory) onto Jalview, and for each PDB file identified:
      a. Search the alignment to detect sequences with similar IDs.
      b. test similarity between PDB sequence and similarly named sequences to find those that are properly contained/contain the PDB sequence.
      c. add associations for strong matches identified in b, and optionally ask the user if they want to add in any of the other files not associated with any sequences.

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          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-860 'view structures' option to open many structures in same window

          • Major - Major loss of function.
          • Resolved

          Improvement - An improvement or enhancement to an existing feature or task. JAL-941 pick best matching PDB chain from many PDBs for a sequence

          • Major - Major loss of function.
          • Open

          Epic - Created by Jira Software - do not edit or delete. Issue type for a big user story that needs to be broken down. JAL-510 sensible behaviour for group file drags/opens

          • Major - Major loss of function.
          • Open

          Bug - A problem which impairs or prevents the functions of the product. JAL-2984 Answering 'No' to PDB Autoassociate dialog doesn't import PDB files

          • Major - Major loss of function.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. JAL-235 Select many PDB files at once when doing 'Associate PDB file with sequence'

          • Critical - Crashes, loss of data, severe memory leak.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1711 allow PDB chain code to be specified when entering a specific PDB ID for a sequence

          • Major - Major loss of function.
          • Closed

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: