vmd-python-rendering

name	vmd-python-rendering
description	Render publication-quality molecular visualizations with vmd-python and Tachyon ray-tracing — environment setup, representations, materials, lighting, camera control, and batch rendering from Python. Use when producing molecular structure or trajectory images programmatically without the VMD GUI.

VMD-Python Molecular Rendering

Render publication-quality molecular visualizations using vmd-python with Tachyon ray-tracing.

Environment Setup

# Create dedicated environment (vmd-python requires Python ≤3.12)
conda create -n vmd-env python=3.12 -y
conda install -n vmd-env -c conda-forge vmd-python tachyon mdanalysis -y

Basic Usage

from vmd import molecule, molrep, display, render, atomsel, axes, evaltcl

# Load structure
molid = molecule.load("psf", "system.psf")
molecule.read(molid, "dcd", "trajectory.dcd", waitfor=-1)
molecule.set_frame(molid, -1)  # Last frame

# Atom selection
sel = atomsel("name CA", molid=molid)
positions = list(zip(sel.x, sel.y, sel.z))  # Direct attribute access
indices = sel.index

# Clear and add representations
while molrep.num(molid) > 0:
    molrep.delrep(molid, 0)

molrep.addrep(molid,
    style="VDW 1.2 20",           # VDW with radius 1.2, resolution 20
    selection="name PT*",
    color="ColorID 2",            # Gray
    material="AOShiny")

molrep.addrep(molid,
    style="CPK 1.0 0.3 20 20",    # CPK: sphere rad, bond rad, resolution
    selection="resname NEC",
    color="Name",                 # Color by atom name
    material="AOShiny")

molrep.addrep(molid,
    style="Licorice 0.15 20 20",  # Bond thickness, resolution
    selection="resname NEC",
    color="ColorID 16",           # Black
    material="AOShiny")

Display Settings

# White background
evaltcl('color Display Background white')

# Turn off axes
axes.set_location('OFF')

# Ambient occlusion (soft shadows)
display.set(ambientocclusion=True, aoambient=0.8, aodirect=0.3)

# Other settings
display.set(depthcue=False, culling=False)

# Camera manipulation via Tcl
evaltcl('display resetview')
evaltcl('scale by 2.5')
evaltcl('rotate x by -30')
evaltcl('rotate y by 45')

display.update()

Rendering

Two-Step Process (Headless)

vmd-python in conda is headless - no OpenGL. Use Tachyon external renderer:

# Step 1: Generate scene file
render.render('Tachyon', 'scene.dat')

# Step 2: Render with tachyon binary
conda run -n vmd-env tachyon scene.dat \
    -res 1920 1080 \
    -aasamples 4 \
    -format TGA \
    -o output.tga

# Step 3: Convert to PNG
from PIL import Image
Image.open('output.tga').save('output.png')

Available Render Methods

from vmd import render
print(render.listall())
# ['ART', 'Gelato', 'PostScript', 'Raster3D', 'Radiance', 'Rayshade',
#  'RenderMan', 'snapshot', 'STL', 'Tachyon', 'POV3', 'VRML-1',
#  'VRML-2', 'Wavefront', 'X3D', 'X3DOM']

Representation Styles

Style	Syntax	Use Case
VDW	VDW radius resolution	Space-filling spheres
CPK	CPK sphere_r bond_r res res	Ball-and-stick
Licorice	Licorice radius res res	Bonds only
NewCartoon	NewCartoon	Protein secondary structure
QuickSurf	QuickSurf radius density gridspacing	Surfaces

Color Options

# By color ID (0-32)
color="ColorID 0"   # Blue
color="ColorID 1"   # Red
color="ColorID 2"   # Gray
color="ColorID 8"   # White
color="ColorID 16"  # Black

# By property
color="Name"        # Element colors
color="Type"        # Atom type
color="ResName"     # Residue
color="Beta"        # B-factor

Materials

Best for Tachyon with AO:

• AOShiny - Reflective with ambient occlusion
• AOChalky - Matte with ambient occlusion
• AOEdgy - Sharp edges with AO

Complete Example

#!/usr/bin/env python3
"""Render molecule on surface with VMD-Python + Tachyon."""

from vmd import molecule, molrep, display, render, atomsel, axes, evaltcl
import subprocess
from PIL import Image

# Load
molid = molecule.load("psf", "system.psf")
molecule.read(molid, "dcd", "traj.dcd", waitfor=-1)
molecule.set_frame(molid, -1)

# Clear reps
while molrep.num(molid) > 0:
    molrep.delrep(molid, 0)

# Add representations
molrep.addrep(molid, style="VDW 1.2 20", selection="name PT*",
              color="ColorID 2", material="AOShiny")
molrep.addrep(molid, style="CPK 0.8 0.2 20 20", selection="resname LIG",
              color="Name", material="AOShiny")

# Display settings
evaltcl('color Display Background white')
axes.set_location('OFF')
display.set(ambientocclusion=True, aoambient=0.8, aodirect=0.3)
evaltcl('display resetview')
evaltcl('scale by 3')
display.update()

# Render
render.render('Tachyon', 'scene.dat')

# External Tachyon render
subprocess.run([
    'tachyon', 'scene.dat',
    '-res', '1920', '1080',
    '-aasamples', '4',
    '-format', 'TGA',
    '-o', 'render.tga'
])

# Convert
Image.open('render.tga').save('render.png')

Limitations

• No TachyonInternal: conda-forge build lacks internal renderer
• Headless only: No interactive display, snapshot renders empty
• Python 3.12 max: Not compatible with Python 3.13+

Tips

1. Use evaltcl() for Tcl commands not exposed in Python API
2. Attribute access (sel.x) preferred over sel.get('x') (deprecated)
3. AOShiny material required for ambient occlusion to work
4. Higher -aasamples = smoother edges but slower render