#128 saved fasta file not correct

v1.5.0.4
closed-fixed
5
2012-08-14
2012-07-24
Anonymous
No

Multiple conformations (at least for the 'CA' atom) of a residue result in multiple instances of a residue in the saved sequence file. This only seems to occur when using the 'save file.fasta' command as opposed to saving an alignment object. E.g. load 3bow, which has two conformations of MET383 of chain A. Save 3bow.fasta and the resulting file has a sequence at that region of TFWMMNP, instead of TFWMNP

Discussion

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    Anonymous - 2012-07-24
    • milestone: --> 2774648
     
  • Jason Vertrees

    Jason Vertrees - 2012-08-14
    • assigned_to: nobody --> inchoate
    • milestone: 2774648 --> v1.5.0.4
    • status: open --> closed-fixed
     
  • Jason Vertrees

    Jason Vertrees - 2012-08-14

    We chose the solution presented in revision 4002. Structures like '1ejg' forbid us to use 'guide' so we chose to use: obj and (alt '' or alt 'A'). Using something like 'guide' will return multiple occurrences of an amino acid if it's listed under a different name (eg. residue 22 in 1ejg is both a PRO and a SER). Using the solution we chose here, you're missing a possible sequence, but the output from the command is at least correct.

    This also fixes the multiple-sequence issue.

     

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