Korak Ray
korakray.bsky.social
Korak Ray
@korakray.bsky.social
Interested in biophysical chemistry, single molecules, and nucleic acids. Into puns and speculative fiction.

Postdoc @Rueda Lab, MRC LMS.

He/him
Congratulations, John! Great to see this out!
June 10, 2025 at 10:53 AM
Congratulations, John!
March 27, 2025 at 10:45 PM
Also make sure you have the latest version of the software for your analysis needs. The software is always being updated. You can find the latest updates at the website gonzalezbiophysicslab.github.io/tmaven/
Also, please follow and take part in the discussions at github.com/GonzalezBiop...
GonzalezBiophysicsLab tmaven · Discussions
Explore the GitHub Discussions forum for GonzalezBiophysicsLab tmaven. Discuss code, ask questions & collaborate with the developer community.
github.com
February 10, 2024 at 12:12 AM
That sounds really interesting and definitely something to try out. Thank you for the suggestion!
October 21, 2023 at 6:22 PM
The meta-analysis is complicated because
a) different software were historically used with other equipment that confound the software's effect.
b) metadata on software in PDB files had inconsistent reporting.

So, our analysis is purely descriptive. With those caveats in mind however, yes, there is
October 20, 2023 at 9:16 PM
(6/6) Our method, which we call HARP, is open-source and freely available as a downloadable application which you can use to test the local resolution and map-to-model agreement of your favourite (or your own!) cryoEM structure! Give it a try! github.com/bayes-shape-...
GitHub - bayes-shape-calc/HARP: Hierarchical Atomic Resolution Perception
Hierarchical Atomic Resolution Perception. Contribute to bayes-shape-calc/HARP development by creating an account on GitHub.
github.com
October 20, 2023 at 7:38 PM
(5/6) We also see how sensitive this framework is to local chemical changes, with specific amino acids that are known to appear distorted in cryoEM maps (Glu, Asp, Cys), showing lower levels of atomic information than similarly sized residues.
October 20, 2023 at 7:38 PM
(4/6)...revealing, e.g., how the cryoEM resolution revolution has lead to increased atomic resolution over the years, and, surprisingly, a seasonal trend in atomic resolution (based on when structures are deposited in the PDB) that seems to correlate with the academic calendar.
October 20, 2023 at 7:37 PM
(3/6) Comparison between the atomic and residue models in particular reveals the extent of local atomic resolution at individual residues. As expected, on average, this local atomic resolution measure correlates with the standard FSC resolution of maps, but yields richer info...
October 20, 2023 at 7:37 PM
(2/6) We utilise the hierarchical nature of biomolecular structure to define models of cryoEM density at different structural levels, which can be used to select the level that agrees best with experimental data, revealing the extent of structural information present in the data.
October 20, 2023 at 7:36 PM
(6/6) Our method, which we call HARP, is open-source and freely available as a downloadable application which you can use to test the local resolution and map-to-model agreement of your favourite (or your own!) cryoEM structure! Give it a try! github.com/bayes-shape-...
GitHub - bayes-shape-calc/HARP: Hierarchical Atomic Resolution Perception
Hierarchical Atomic Resolution Perception. Contribute to bayes-shape-calc/HARP development by creating an account on GitHub.
github.com
October 20, 2023 at 7:33 PM
(5/6) We also see how sensitive this framework is to local chemical changes, with specific amino acids that are known to appear distorted in cryoEM maps (Glu, Asp, Cys), showing lower levels of atomic information than similarly sized residues.
October 20, 2023 at 7:32 PM
(4/6)...revealing, e.g., how the cryoEM resolution revolution has lead to increased atomic resolution over the years, and, surprisingly, a seasonal trend in atomic resolution (based on when structures are deposited in the PDB) that seems to correlate with the academic calendar.
October 20, 2023 at 7:32 PM
(3/6) Comparison between the atomic and residue models in particular reveals the extent of local atomic resolution at individual residues. As expected, on average, this local atomic resolution measure correlates with the standard FSC resolution of maps, but yields richer info...
October 20, 2023 at 7:31 PM
(2/6) We utilise the hierarchical nature of biomolecular structure to define models of cryoEM density at different structural levels, which can be used to select the level that agrees best with experimental data, revealing the extent of structural information present in the data.
October 20, 2023 at 7:30 PM