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Visualize molecular systems and analyze MD trajectories and hydrate cages headlessly.
Copy the install command and let the AI configure it · recommended for beginners
No copy-paste install info for "pymol-mcp" yet — see the docs or source repo.
Use pymol-mcp in headless mode to load a PDB structure, apply a style suitable for showing protein-ligand interactions, and export a high-resolution image.
Produces the molecular visualization and exports an image suitable for reports or papers.
Use pymol-mcp to read a GROMACS or LAMMPS molecular dynamics trajectory, inspect conformational changes frame by frame, and output a summary of key observations.
Provides trajectory visualization and a summary of conformational changes to help interpret the simulation.
Use pymol-mcp to analyze a clathrate hydrate system, identify cages with TRACE, calculate occupancy, and inspect the hydrogen-bond network and F3/F4 order parameters.
Outputs cage identification, occupancy analysis, and related structural order metrics.
Researchers can run this tool on compute nodes without a desktop environment to load, render, and export molecular structures. It fits automated visualization workflows in remote computing environments.
Users working on molecular simulations can use it to read GROMACS or LAMMPS trajectories and observe structural changes over time. It is useful for reviewing simulation outputs and performing initial interpretation.
For clathrate hydrate research, the tool can analyze hydrogen-bond networks, F3/F4 order parameters, and TRACE-based cage perception and occupancy. It suits studies focused on microscopic structure and cage occupancy behavior.
It is an MCP tool built around headless PyMOL for molecular visualization, molecular dynamics trajectory handling, and clathrate hydrate analysis. Known capabilities include hydrogen-bond networks, F3/F4 order parameters, and TRACE cage perception with occupancy analysis.
The provided information indicates support for GROMACS and LAMMPS molecular dynamics trajectories. For specific file formats and usage details, see the source repository.
From the available material, we can only confirm that it is related to headless PyMOL. For installation steps, runtime dependencies, or extra configuration requirements, see the source repository.
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