# wjgoarxiv/vmd-hydrate-mcp

Source: https://glimind.com/server/glama%2Fwjgoarxiv%2Fvmd-hydrate-mcp
Registry id: `glama/wjgoarxiv/vmd-hydrate-mcp`
Status: unknown

## Tools (17)

- `add_representation`: Layer another representation (multi-rep views)
- `clear_representations`: Remove all representations
- `hbond_network`: Water H-bond network + coordination
- `hydrate_order_params`: F3 + F4 water order parameters
- `identify_cages`: Cage counts (5¹²/5¹²6⁴/…) + sI/sII/sH structure
- `list_molecules`: List loaded molecules
- `load_structure`: Load a structure/trajectory (returns a molid)
- `measure_geometry`: Distance / angle / dihedral by atom index
- `radius_of_gyration`: Rg of a selection
- `render`: Headless PNG of the current view
- `render_cages`: Photorealistic cage render (AO+shadows, ortho); filter / recolor / emphasize cages by prompt
- `reset_view`: Live camera control (visible in GUI mode)
- `resolve_selection`: Atom count for a selection (catches the 0-atom .gro trap)
- `rotate_view`: Live camera control (visible in GUI mode)
- `set_representation`: Style/color/material/selection for a molecule (replaces reps)
- `vmd_status`: VMD version + molecules loaded in the live session
- `zoom_view`: Live camera control (visible in GUI mode)

Measured by Glimind (https://glimind.com): MCP handshake + tool list only, no tool is ever called. CC BY 4.0.