Dear all,
As announced previously, wwPDB validation of 3DEM structures for which
there is both a model and an EM volume will now 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
similarity of the map values around each atom relative to a
Gaussian-like function for a well resolved atom. 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 color-mapped onto ribbon models with views from
three orthogonal directions. Similar images will also be introduced to
visualize the per-residue atom-inclusion scores. Comparison of these two
sets of images will assist in visual assessment of the model-to-map fit
and quality.
To see example images of models where residues are colored according to
their Q-score, please visit the news page on the wwPDB website:
http://www.wwpdb.org/news/news?year=2022#63288a46831916e52206a1f0
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
(https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Items/_pdbx_vrpt_summary_entity_geometry.average_residue_inclusion.html)
and _pdbx_vrpt_model_instance_geometry.residue_inclusion
(https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_vrpt.dic/Items/_pdbx_vrpt_model_instance_geometry.residue_inclusion.html)
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:
http://www.wwpdb.org/validation/2017/EMValidationReportHelp
- EM map-only:
http://www.wwpdb.org/validation/2017/EMMapValidationReportHelp
- EM tomograms:
http://www.wwpdb.org/validation/2017/EMTomogramValidationReportHelp
If you have any questions or queries about wwPDB validation, please
contact us at [email protected].
Kindest regards,
Deborah Harrus.
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Deborah Harrus, Ph.D.
Lead Annotator
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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