Python code

py3Dmol

Description

• To visualize molecular structures in 3D.
• Interactive: Real-time manipulation (rotate, zoom).
• Customizable: Various styles (stick, sphere, cartoon) and colors.
• Ease of Use: Simple API for Python users.
• Ideal for Jupyter Notebooks.
• Open Source [py3Dmol GitHub webpage]

Examples

Example 1 (cortisol) input

#cortisol
import py3Dmol

view = py3Dmol.view(query='cid:5754')

view.setStyle({'stick': {'color':'spectrum'}})
view.zoomTo()
view.render()

Example 1 (cortisol) output

Example 2 (CBG) input

# CBG
import py3Dmol

view = py3Dmol.view(width=800, height=800, query='pdb:2V95', viewergrid=(2,2), linked=True)

view.setStyle({'cartoon': {'color': 'spectrum'}}, viewer=(0,0))

view.setStyle({'cartoon': {'color': '#4aa6ff', 'style': 'parabola'}}, viewer=(0,1))

view.addSurface(py3Dmol.VDW, {'opacity': 0.5}, viewer=(0,0))
view.setStyle({'cartoon': {'color': 'spectrum'}}, viewer=(1,0))
view.setStyle({'elem': 'Zn'}, {'sphere': {'scale': 2.0}}, viewer=(1,0))
view.setStyle({'stick': {'colorscheme': 'cyanCarbon'}}, viewer=(1,1))


view.setBackgroundColor('#ebf4fb', viewer=(0,0))
view.setBackgroundColor('#ebf4fb', viewer=(0,1))
view.setBackgroundColor('#ebf4fb', viewer=(1,0))
view.setBackgroundColor('#ebf4fb', viewer=(1,1))

view.zoomTo()
view.render()

Example 2 (CBG) output

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