[PyMOL] cmd.align does not work

[Tereza Č. <ter...@na...>]

Hello,
I am trying to use the Pymol API to align some structures with the
`cmd.align` command.
It seems that it does not work correctly though.
I have made a picture before running the `cmd.align` and after running it,
the pictures look the same.
Before alignment: https://pasteboard.co/1RtHTgy7iOKC.png/
[image: test_nonaligned.png]
After alignment: https://pasteboard.co/ta0YVyaLbaE4.png
[image: test_aligned.png]

When I use the Pymol user interface on the same computer and I align the
same structures, they align very well.
Aligned: https://pasteboard.co/gr2hsa8whb47.png
[image: aligned_structures.png]

The version of Pymol I am using: pymol-2.3.4
Here is the script which I used:

#!/bin/env python

from pymol import cmd
import os

cmd.load('tps_structures/' + 'A0A140AZ69' + '.pdb')
cmd.load('tps_structures/' + 'A0A140AZ72' + '.pdb')

cmd.show_as('cartoon')

cmd.spectrum( "resi", "rainbow", 'A0A140AZ69')
cmd.spectrum( "resi", "rainbow", 'A0A140AZ72')
cmd.png(os.path.join('test_nonaligned' + '.png'), 1200, 1200, 300, 1)

reference = 'A0A140AZ69'
cmd.align(reference, 'A0A140AZ72', cutoff=2.0, cycles=20, quiet=0)
cmd.png(os.path.join('test_aligned' + '.png'), 1200, 1200, 300, 1)

cmd.hide('cartoon', 'A0A140AZ69')
cmd.hide('cartoon', 'A0A140AZ72')

cmd.show_as('cartoon', 'A0A140AZ69')
cmd.png(os.path.join('test_aligned_A0A140AZ69' + '.png'), 1200, 1200, 300, 1
)
cmd.hide('cartoon', 'A0A140AZ69')

cmd.show_as('cartoon', 'A0A140AZ72')
cmd.png(os.path.join('test_aligned_A0A140AZ72' + '.png'), 1200, 1200, 300, 1
)
cmd.hide('cartoon', 'A0A140AZ72')

I appreciate any help on how to make the cmd.align work.
Thank you

Tereza
-- 
Tereza Čalounová

Charles University
Faculty of Science
Albertov 6, 128 43 Praha 2
www.natur.cuni.cz/en