Is there a way write a script in python to use "super" to align proteins from a 2D array? Each row of the array has 2 columns, and for each row, I want to "super" the two proteins (one in each column)

  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Aug 26, 2022 at 2:08
  • $\begingroup$ What do you mean by super? Is it this? $\endgroup$
    – gringer
    Aug 27, 2022 at 9:41

1 Answer 1


You can use Python "normally" and import the pymol module. In the script that holds the proteins in your matrix, you can add a function that does the super alignment.

To use it, in your console type pymol -cq this_script_name.py.

You need to have pymol installed and accessed via console. Easiest way I found to manage it is to create a new environment via conda and install pymol there.

import pymol

def super_prots(prot_1, prot_2):
    pymol.cmd.fetch(prot_1, 'prot_1')
    pymol.cmd.fetch(prot_2, 'prot_2')

    # If you are using already downloaded pdb files, use load instead:
    # pymol.cmd.load(prot_1, 'prot_1')
    # pymol.cmd.load(prot_2, 'prot_2')

    pymol.cmd.set('ray_opaque_background', 0)

    # Show cartoon and paint them different
    pymol.cmd.show('cartoon', 'prot_1')
    pymol.cmd.color('orange', 'prot_1')
    pymol.cmd.show('cartoon', 'prot_2')
    pymol.cmd.color('lightblue', 'prot_2')

    # Align both proteins
    pymol.cmd.super('prot_1', 'prot_2')

    # Improve image quality, and get png.
    pymol.cmd.set('depth_cue', 0)
    pymol.cmd.set('spec_reflect', 0)
    pymol.cmd.set('cartoon_sampling', 15)
    pymol.cmd.set('ribbon_sampling', 15)
    pymol.cmd.set('antialias', 2)

    # This creates high-quality images, but might take a long time to
    # process. Adjust parameters accordingly.

if __name__ == '__main__':
    # These are entries from PDB. It can work with already downloaded
    # files, but you have to change the function accordingly
    protein_matrix = [['1EWL', '4W5B'],
                      ['4E2D', '3ATZ'],
    for prot_1, prot_2 in protein_matrix:
        super_prots(prot_1, prot_2)

This will generate .png images of the alignment, but you can also ask it to save the alignment into .pdb files adding pymol.cmd.save(f'{prot_1}_{prot_2}.pdb')

The commands' documentation can be found here.


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