Return the VMD version/banner and the resolved launcher path. Use this first to confirm the server can reach a working VMD.

Load a structure (and optional trajectory) and report a summary: total atoms, number of frames, protein/water/backbone atom counts, and the number of distinct chains and residues.

Count atoms matching a VMD atom-selection expression (e.g. "protein and name CA", "resname LIG", "within 5 of protein").

Radius of gyration (nm-scale, in VMD's Angstrom units) of a selection, computed for every frame. Returns a per-frame series plus min/max/mean.

RMSD of a selection across a trajectory relative to a reference frame.

With align=True each frame is first least-squares fitted onto the reference (rigid-body alignment) before measuring RMSD. Returns a per-frame series plus min/max/mean (Angstrom).

Solvent-accessible surface area (Angstrom^2) of a selection, per frame. srad is the solvent probe radius (1.4 A ~ water).

Per-atom root-mean-square fluctuation (RMSF) across a trajectory.

Returns one row per selected atom plus min/max/mean RMSF in Angstrom. Use selections such as "protein and name CA" for compact per-residue traces.

Distance between the centers of two atom selections.

By default the distance is measured at one frame. Set all_frames=True to return a per-frame series for a trajectory.

Find atom-index contact pairs between two selections at one frame.

cutoff is in Angstrom. The total contact count is always returned; the explicit pairs list is clipped to max_pairs to keep MCP responses bounded.

Ray-trace a molecular image HEADLESSLY with VMD's built-in Tachyon and save it as PNG (no display needed).

representation is one of the supported VMD draw methods; coloring is one of the supported VMD color methods. The image is written under VMD_MCP_ROOT by default. Absolute output paths are rejected unless VMD_MCP_ALLOW_ABSOLUTE_OUTPUTS=1 is set.

Render a molecule using a curated publication-oriented visual preset.

Presets reduce brittle representation/coloring choices while still allowing a custom atom selection when needed.

Run an ARBITRARY VMD Tcl script headlessly and return its combined stdout/stderr plus any parsed @@VMDMCP@@ marker lines.

Emit results from your script with: puts "@@VMDMCP@@ key=value ...". Use this for any analysis not covered by a dedicated tool (measure hbonds, measure contacts, custom per-residue loops, cluster analysis, ...). End the script with quit.