**Source:**
The structural snapshots come from a molecular dynamics (MD) simulation trajectory of a protein system. The trajectory frames were generated using standard MD simulation software and exported as structural snapshots at regular time intervals. The motion values visualized here were calculated per residue from the trajectory coordinates.
**Tool:**
The visualization was generated using tools I developed called RMSX and Flipbook. RMSX is a time-resolved extension of RMSF that measures per-residue motion across the trajectory. The Flipbook component renders sequential structural snapshots where motion magnitude is encoded using both color and backbone thickness.
**Methods / Code:**
The analysis pipeline is written in Python and uses **MDAnalysis** for trajectory processing and calculation of motion metrics. The rendering of structural snapshots is automated using scripting in ChimeraX and VMD to arrange frames and apply color/thickness encoding.
The goal of this visualization approach is to make molecular dynamics trajectories easier to interpret in static figures (e.g., for papers or posters) rather than relying solely on movies.
1 Comment
**Source:**
The structural snapshots come from a molecular dynamics (MD) simulation trajectory of a protein system. The trajectory frames were generated using standard MD simulation software and exported as structural snapshots at regular time intervals. The motion values visualized here were calculated per residue from the trajectory coordinates.
**Tool:**
The visualization was generated using tools I developed called RMSX and Flipbook. RMSX is a time-resolved extension of RMSF that measures per-residue motion across the trajectory. The Flipbook component renders sequential structural snapshots where motion magnitude is encoded using both color and backbone thickness.
**Methods / Code:**
The analysis pipeline is written in Python and uses **MDAnalysis** for trajectory processing and calculation of motion metrics. The rendering of structural snapshots is automated using scripting in ChimeraX and VMD to arrange frames and apply color/thickness encoding.
GitHub repository (code and scripts):
[https://github.com/AntunesLab/rmsx](https://github.com/AntunesLab/rmsx)
The goal of this visualization approach is to make molecular dynamics trajectories easier to interpret in static figures (e.g., for papers or posters) rather than relying solely on movies.