Visualizing 3D Structures

To view your predicted structure generated by AlphaFold in 3D, you can use Visual Molecular Dynamics (VMD).

Steps:

• Log onto Open On Demand ( https://rivanna-portal.hpc.virginia.edu/)
• Choose the ‘Desktop’ interactive app and fill out the webform with your required resources.
• Click launch.
• Load VMD in the terminal:

module load vmd
vmd

The VMD windows will launch. From there, you can open your .pdb file from the AlphaFold output directory to view the 3D model (colored by pLDDT).