Changes between Version 1 and Version 2 of Ticket #16207, comment 1


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Timestamp:
Oct 28, 2024, 4:33:33 PM (13 months ago)
Author:
Tom Goddard

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  • Ticket #16207, comment 1

    v1 v2  
    11Foldseek is a bit wacky.  The output as visible in the .sms file ChimeraX saves in ~/Downloads/ChimeraX/Foldseek/1hxz_foldseek_pdb.sms indicates where the problem likes.  The Foldseek pdb100 database is using PDB biassembly files so the two 1hxz_D entries are listed in the Foldseek output as 1hxz-assembly1.cif.gz_D and 1hxz-assembly1.cif.gz_D-2.  If you create the assembly from the 1hxz mmcif it is a dimer with two copies of chain D.  Foldseek should filter this out since they are identical but apparently does not.
    22
    3 I can filter these out.  My guess is that they are not filtered out because Foldseek can do multimeric searches and in that case duplicate changes may have different packing and so all copies may be needed to find a matching complex.
     3I can filter these out.  My guess is that they are not filtered out because Foldseek can do multimeric searches and in that case duplicate chains may have different packing and so all copies may be needed to find a matching complex.