Dear Colleagues,
Starting September 23, wwPDB validation of 3DEM structures for which
there is both a model and an EM volume will include the Q-score metric
(Pintilie, G., et al., 2020, Nat. Methods). This follows recommendations
from the wwPDB/EMDB workshop on cryo-EM data management, deposition and
validation in 2020 (white paper in preparation), as well as EM
Validation Challenge events (Lawson C., et al., 2020, Struct. Dyn.;
Lawson, et al., 2021, Nat. Methods). This will be the first quantitative
parameter of residue and chain resolvability for EM maps in wwPDB
validation reports and will provide an additional map-model assessment
criterion.
The Q-score calculates the resolvability of atoms by measuring the
similarity of the map values around each atom relative to a
Gaussian-like function for a well-resolved atom. A Q-score of 1
indicates that the similarity is perfect whilst closer to 0 indicates
the similarity is low. If the atom is not well placed in the map then a
negative Q-score value may be reported. Therefore, Q-score values in the
reports will be in a range of -1 to +1.
The wwPDB EM validation reports will provide Q-scores for single
particle, helical reconstruction, electron crystallography, and
subtomogram averaging entries for which both an EM map and coordinate
model have been deposited.
Validation reports (PDF files) will contain images of the average
per-residue Q-scores colour-mapped onto ribbon models with views from
three orthogonal directions. Similar images will also be introduced to
visualize the per-residue atom-inclusion scores. A comparison of these
two sets of images will assist in the visual assessment of the
model-to-map fit and quality.
Please refer to the wwPDB news article for example images:
http://www.wwpdb.org/news/news?year=2022#62de9e5235ec5bb4ddb19a43
The validation reports will also contain a table of average per-chain
values of both metrics (Q-score and atom inclusion) as well as their
overall average values for the entire model.
The per-residue and the per-chain average atom-inclusion and Q-score
values will also be provided in the mmCIF and XML formatted validation
files. The mmCIF categories _pdbx_vrpt_summary_entity_fit_to_map and
_pdbx_vrpt_model_instance_map_fitting will be introduced to include both
the Q-scores and atom-inclusion values. The existing items,
_pdbx_vrpt_summary_entity_geometry.average_residue_inclusion and
_pdbx_vrpt_model_instance_geometry.residue_inclusion for atom inclusion
will no longer be used.
The PDB Core Archive holds validation reports that assess each 3DEM
model in the PDB along with the associated experimental 3D volume in
EMDB. Validation reports of 3DEM structures (map and model) can be
downloaded at the following wwPDB mirrors:
* wwPDB: https://ftp.wwpdb.org/pub/pdb/validation_reports/
* RCSB PDB: https://ftp.rcsb.org/pub/pdb/validation_reports/
* PDBe: https://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/
* PDBj: https://ftp.pdbj.org/pub/pdb/validation_reports/
The EMDB Core Archive holds validation reports that assess each EMDB
map/tomogram entry. Validation reports for all EMDB volumes can be
downloaded at the following wwPDB mirrors:
* EMDB: https://ftp.ebi.ac.uk/pub/databases/emdb/validation_reports/
* wwPDB: https://ftp.wwpdb.org/pub/emdb/validation_reports/
* RCSB PDB: https://ftp.rcsb.org/pub/emdb/validation_reports/
* PDBj: https://ftp.pdbj.org/pub/emdb/validation_reports/
Additional information about validation reports is available for EM
map+model, EM map-only, and EM tomograms.
If you have any questions or queries about wwPDB validation, please
contact us at [email protected].
Best regards,
James Tolchard
--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544
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