[3dem] [EXTERNAL] Re: New game to learn/train cryo-EM/ET map resolution recognition

Wed Apr 22 00:31:43 PDT 2026

My guess is that the game low-pass filters the map. If you go to the PDB code give at the end, it is always at higher resolution than the correct option in the game. I guess they decided to use high-resolution structures, so that they could have the options to show backbone and sidechains.

This is a wonderful educational tool. I sometimes use images of maps to train users and challenge them to guess the resolution, based on map features. But I have some feedback and suggestion for improvements:

- Real maps never look this good, due to anisotropy, flexibility/disorder, solvent etc. To make the maps look more realistic, consider including B-factor, Q-score and radial blurring (due to misalignments, e.g. average a few randomly rotated maps) when calculating the synthetic maps. Or filter based on local-resolution estimation.
- Consider using the real maps instead of calculated maps. Where there is no PDB model and only an EMDB entry, then you can disable the backbone/sidechain options.
- A bit too many low-resolution cases for my taste. Perhaps add a toggle to have fewer low-resolution maps? To me, with a focus on single-particle, I never really have to care about the difference between 15 and 20 Å (other than making masks).
- Add more levels at high resolution.
- The hard mode should not be based on time, but instead smaller differences in the resolution steps. It would be more interesting to try differentiating between high-resolution details, e.g. 1.5-2.0 Å (hole in aromatic rings), 2.0-2.5 Å (water molecules, carbonyl oxygens), 2.5-3.0 Å (small sidechains), 3.0-3.5 Å (most sidechains), 3.5-4 Å (large sidechains), 5-6 Å (cork-screw alpha helices), 7-9 Å (sausage alpha helices).

Anyways, great job!

Regards,
Daniel

From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Reza Khayat via 3dem <3dem at ncmir.ucsd.edu>
Reply to: Reza Khayat <rkhayat at ccny.cuny.edu>
Date: Tuesday, 21 April 2026 at 19:27
Cc: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>, "CCPEM at jiscmail.ac.uk" <CCPEM at jiscmail.ac.uk>
Subject: Re: [3dem] [EXTERNAL] Re: New game to learn/train cryo-EM/ET map resolution recognition

This is an important tool. How did you determine the resolution? Did you calculate it or is it experimental? Perhaps next version should include anisotropy for SPA and missing wedge for STA. Also, the 20 and 15Angstroms may be too close to distinguish for a beginner. In fact, being able to reach sub-nanometer was a blessing because it allowed us to move beyond the twilight zone.

Best wishes,
Reza
________________________________
From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Ayil Perrott via 3dem <3dem at ncmir.ucsd.edu>
Sent: 21 April 2026 12:58 PM
To: Leandro F. Estrozi <leandro.estrozi at ibs.fr>
Cc: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>; CCPEM at jiscmail.ac.uk <CCPEM at jiscmail.ac.uk>
Subject: [EXTERNAL] Re: [3dem] New game to learn/train cryo-EM/ET map resolution recognition

Leandro,

This game is amazing! I just played a few rounds on my lunch break and had so much fun! I think this is a wonderful tool to help students and beginners get more familiar with looking at structures, I even found myself learning a thing or two about it.

What are your plans for expanding this game, that is, beyond including noise in the maps? Do you have any plans for identifying point symmetry/asymmetry, structural heterogeneity, classification based on structural (dis)similarity, etc.? I think those would be really good additions as well, especially for helping train the eyes of newbies.

Wonderful job, and can't wait to see how you expand upon it!

Sincerely,
Ayil Perrott
(they/them)
--
Doctoral Student
Department of Cellular, Molecular, and Genetic Medicine
Virginia Commonwealth University
Richmond, VA

El mar, 21 abr 2026, 12:44, Leandro F. Estrozi via 3dem <3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>> escribió:
Dear colleagues,

I am pleased to share a new online training game designed for newcomers
in structural biology, with a focus on cryo-EM and cryo-ET map
interpretation:

https://urldefense.com/v3/__https://rico.ibs.fr/helixplorer/resolution/__;!!Mih3wA!EJvDy_wVZYtD-rptRWtrUxbq7A8pGA1ZjbK_kAX9nYpXHYtdekjFvrioD4obUpLP_o_2rpttEOrdDSTtQBS4juXqBm9W$<https://urldefense.com/v3/__https:/rico.ibs.fr/helixplorer/resolution/__;!!Mih3wA!EJvDy_wVZYtD-rptRWtrUxbq7A8pGA1ZjbK_kAX9nYpXHYtdekjFvrioD4obUpLP_o_2rpttEOrdDSTtQBS4juXqBm9W$>

A common challenge in the field is learning to recognize whether a 3D
map is consistent with a given resolution estimate. Confusing, for
example, a 4 Å map with an 8 Å map can lead to substantial time loss
during model building and interpretation. This game was created to help
users develop an intuition for the structural features visible across
the range of resolutions typically obtained in cryo-EM/ET.

It is aimed mainly at students and beginners, but others may also find
it fun or useful as a quick training exercise.

I should note that I am fully aware that noise plays an important role
in real cryo-EM/ET data, and this first version of the game does not yet
include noise.

Feedback is very welcome. Please feel free to share it with anyone who
might be interested.

Best regards,

Leandro.

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