Complex Water Networks Visualized by Cryogenic Electron Microscopy of RNA

Repository accompanying the manuscript:

[preprint]

Rachael C. Kretsch, Shanshan Li, Grigore Pintilie, Michael Z. Palo, David A. Case, Rhiju Das, Kaiming Zhang, Wah Chiu. Complex Water Networks Visualized through 2.2-2.3 Å Cryogenic Electron Microscopy of RNA. bioRxiv 2025.01.23.634578; doi: https://doi.org/10.1101/2025.01.23.634578

Maps and models

The atomic coordinates used in this study can be found in models. The code for the automated identification of water and ions used in this work to create the models used in this repository can be found at, SWIM they were based on https://github.com/gregdp/segger.

Molecular dynamics

Simulation input files, analysis, links for raw simulations, and data files used in analysis elsewhere in this repository can be found in simulations.

Analysis

All required data to recreate figures is included in this repository, in order to recreate these files, scripts in the analysis. Code to create figures of atomic models are maps can be found in chimerax_code. See README in those respective folders for more details.

Locations of graphing code:

• Fig 2A-B models_water_mg_by_consensus.cxc
• Fig 2C-E consensus_nonconsensus_compare.ipynb
• Fig 4A-B get_MD_density_values.ipynb
• Fig 5 Visualize_water_networks
• ED Fig 1H-I Bfactor-plot.ipynb
• ED Fig 2C Qscore_22_23_31.ipynb
• ED Fig 3A-D localres_rmsd_rmsf_q.cxc
• ED Fig 3E nucleotide_v_qscore_rmsf.ipynb
• ED Fig 3F-H per_residue_correlations.ipynb
• ED Fig 4I swim_criteria_compare
• ED Fig 4L,M consensus_nonconsensus_compare.ipynb
• ED Fig 4J,K,N,O SWIM_summary_Qscore_distances.ipynb
• ED Fig 5A-E models_water_mg_by_agreement.cxc
• ED Fig 5F-G water_mg_consensus_tables.ipynb
• ED Fig 7B-D interaction_types.ipynb
• ED Fig 7E avg_around_nuc
• ED Fig 8A,B categorize_water_ions.ipynb
• ED Fig 9A,C,D,F MD_summary_plots.ipynb
• ED Fig 9E get_MD_density_values.ipynb
• Supp Table 1 categorize_water_ions.ipynb

Revision response tables or figures

• Response #3.1 - running SWIM on half maps swim_criteria_compare
• Response #3.5 - Q-score waters based on binding base vs backbone consensus_nonconsensus_compare.ipynb