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AlphaFold uses the wrong resolution field during structure parsing #915
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ljarosch
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Mar 21, 2024
Without the break statement this will fall back to setting the resolution to _reflns.d_resolution_high for most structures, which reflects the resolution limit in the raw data and not the final structure (see https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.d_resolution_high.html and https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_d_res_high.html). Fixes google-deepmind#915
This was referenced Mar 21, 2024
Thanks for reporting, this is indeed a bug and I will send a fix. |
Fixed in 6d95d19. Thanks again! |
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AlphaFold uses these lines for parsing the resolution of structures:
This means that effectively _reflns.d_resolution_high will be used to set resolution whenever it is available, however this reflects the resolution limit in the raw data and not the final PDB model (see https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.d_resolution_high.html), effectively overestimating the resolution for many structures. Instead, _refine.ls_d_res_high should be used (https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_d_res_high.html).
It's likely that this was the intended behavior but the loop is missing a break statement in the try-block.
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