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PDBDEV_00000001.cif has incorrect ihm_external_files data #68

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tomgoddard opened this issue Jul 27, 2018 · 2 comments
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PDBDEV_00000001.cif has incorrect ihm_external_files data #68

tomgoddard opened this issue Jul 27, 2018 · 2 comments

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@tomgoddard
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PDBDev entry 01 fails to open in ChimeraX giving an unknown file type error because of incorrect data in the ihm_external_files table. Specifically ihm_external_files rows 29-35 which are localization map files have reference_id 2 (in column 2) and instead it should be reference_id 5. Reference id 2 in defined in ihm_external_reference_info is https://zenodo.org/record/1218053/files/clus.1.aligned.dcd while reference id 5 is where the localization map files are found.

Entry validation should certainly verify that all external files exist.
benmwebb added a commit to integrativemodeling/nup84 that referenced this issue Jul 27, 2018
@benmwebb
Uniquely name our IHM repositories
cadad7c 
Previously we called both of the Repository objects
used in this loop 'r', which caused one to overwrite
the other, such that files ended up pointed to the
wrong URLs. Relates ihmwg/IHMCIF#68.
@tomgoddard tomgoddard mentioned this issue Jul 27, 2018
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@tomgoddard
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Has the fix to PDBDev 01 been pushed to the PDBDev web site? Kai Kammer reports it still does not open in ChimeraX.

@brindakv
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Yes, it is updated now.

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@tomgoddard @brindakv