[3dem] Introducing the first 3DEM Model-Map percentile slider to the wwPDB validation report

[Greg Pintilie]

Thank you too Kyle, and indeed Zhe, who bravely kicked off the integration into the reports quite some time ago. It’s been a process I’m sure, and so nice to see it come to fruition.

And indeed there is more to do, as you know we have plans on making it easier to use. I noted that the announcement said it is "the first 3DEM Model-Map percentile slider”, and so hopefully not the last. 

It is also good to see model building and validation is still a topic at many workshops, and I have seen many announcements with exciting agendas. 

Perhaps I can do a shout out to Omar Davulcu who organized a really nice one at PNCC, mostly remote, with very large attendance... some recordings are here:
https://urldefense.com/v3/__https://www.youtube.com/@pacificnorthwestcryoemcenter__;!!Mih3wA!AN4B1jxHH16peHQhAdn4pBuKC3DTr07_3c1acq4FV2SbTU0iSag1wh8EQ2biMI1fTX3555U5hRiHeowT$ 

We have one coming up at Stanford-SLAC at the end of October, though registrations are closed now, hopefully some had the chance to register already, or look out for presentations to be posted after.
https://urldefense.com/v3/__https://s2c2.slac.stanford.edu/training/workshops-lectures/workshop-lecture-archive__;!!Mih3wA!AN4B1jxHH16peHQhAdn4pBuKC3DTr07_3c1acq4FV2SbTU0iSag1wh8EQ2biMI1fTX3555U5hVlAPIui$ 

Let’s keep going!

With kind regards,

Greg P.



> On Sep 26, 2025, at 8:10 AM, Kyle Morris <kyle at ebi.ac.uk> wrote:
> 
> Thanks for the collaboration Greg, particularly with Zhe at the EMDB. Thanks to the worldwide OneDep development and curation team to implement, test and bring this to wwPDB validation reports.
> 
> Here’s to the implementation of tools that will help manuscript reviewers and the community evaluate the data they are handling. More to do, onwards!
> 
> Best wishes,
> Kyle
> 
> EMDB Team Leader | wwPDB principal investigator
> 
>> On 25 Sep 2025, at 17:50, Greg Pintilie via 3dem <3dem at ncmir.ucsd.edu> wrote:
>> 
>> 
>> Hi Justin,
>> 
>> Thank you for this announcement and for your efforts to make this happen. It has been great to collaborate will all at EMDB/EBI and wwPDB on this. It certainly came about thanks to the efforts of many, inspired by the various challenges and workshops that brought many together to discuss these topics.
>> https://urldefense.com/v3/__https://www.emdataresource.org/challenges__;!!Mih3wA!AN4B1jxHH16peHQhAdn4pBuKC3DTr07_3c1acq4FV2SbTU0iSag1wh8EQ2biMI1fTX3555U5hQY7CO7c$  <https://urldefense.com/v3/__https://www.emdataresource.org/challenges__;!!Mih3wA!Cpk6rXHVuu0gDlxssQu-SPFcCy-wHc9ssu3Rz9WSq608xsW3oh0gZZfhU8RM4n2DbWeg6EGVp76lIz2U$>
>> 
>> As a small anecdote, the name Q-score was coined by Wah Chiu, circa 2020, at a validation workshop in Hinxton, UK, while brainstorming how to test if atoms are really resolved in the then-new atomic resolution maps that just came out from various groups.
>> https://urldefense.com/v3/__https://www.ebi.ac.uk/pdbe/news/cryoem-archiving-and-validation-recommendations__;!!Mih3wA!AN4B1jxHH16peHQhAdn4pBuKC3DTr07_3c1acq4FV2SbTU0iSag1wh8EQ2biMI1fTX3555U5hf6uoqFF$  <https://urldefense.com/v3/__https://www.ebi.ac.uk/pdbe/news/cryoem-archiving-and-validation-recommendations__;!!Mih3wA!Cpk6rXHVuu0gDlxssQu-SPFcCy-wHc9ssu3Rz9WSq608xsW3oh0gZZfhU8RM4n2DbWeg6EGVp2TIVGLW$>
>> 
>> We then realized it works ok for lower resolutions too. The correlation to resolution was maybe initially surprising, then we realized it can be rather useful. Hoping this will continue to be useful as a guide for map-model fit and resolvability.
>> 
>> With kind regards,
>> 
>> Greg P.
>> 
>> 
>>> On Sep 25, 2025, at 8:55 AM, Justin Flatt via 3dem <3dem at ncmir.ucsd.edu> wrote:
>>> 
>>> Dear all,
>>> 
>>> The wwPDB is continuing to improve and expand our validation offerings with a new addition to the wwPDB PDF validation reports. Building on the success of the coordinate‑model percentile sliders, which help depositors, reviewers, and archive users assess PDB model quality in the context of the PDB archive, we are now extending this section to include a Q-score percentile slider. The new slider is the first to empower users of this report to assess model-map quality at a glance relative to the EMDB/PDB archives.
>>> 
>>> Starting October 01, newly released 3DEM entries will include the Q‑score percentile slider in its own section below the current sliders under “Overall quality at a glance.” The slider compares an entry’s average Q‑score against both the entire EMDB/PDB archive and a resolution‑similar subset. Because Q‑score correlates strongly with resolution between 1–10 Å, the percentile helps check whether a reported global resolution is reasonable; unusually low values can flag model–map fit or map quality issues. A dedicated Q‑score section supports deeper review with residue‑level mapping to the coordinate model and per‑chain tables.
>>> 
>>> In the near future, wwPDB will re-generate validation reports with Q-score slider for all existing entries in the PDB archive.
>>> 
>>> We are excited for our users to get their hands on this new validation metric. If you have any queries or feedback please let us know at info at wwpdb.org <mailto:info at wwpdb.org>.
>>> 
>>> Please find the full news here: https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2025*68c9b3a1829c3fea8eaf394d__;Iw!!Mih3wA!AN4B1jxHH16peHQhAdn4pBuKC3DTr07_3c1acq4FV2SbTU0iSag1wh8EQ2biMI1fTX3555U5hTjLhFHB$  <https://urldefense.com/v3/__https://www.wwpdb.org/news/news?year=2025*68c9b3a1829c3fea8eaf394d__;Iw!!Mih3wA!DmzD26nwdND2Y8FsQX1esfuCAcC4AppFx54gWMKTbAUk9j8bH2QUAqBEXm37AU5qgbetrnlYqLM9wRws1ZTiAjLF$>
>>> 
>>> Best wishes,
>>> Justin Flatt on behalf of the wwPDB
>>> 
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