compare the predicted and actual structure

[mukulem]

Hi, I was wondering which python library did you use to compare the predicted and actual structure.

something similar to this.

Thanks

[Shenggan]

PyMOL can align and visualize the structure from pdb file.

[mukulem]

Thank you so much for your response, i am trying since yesterday but couldn't figure out how to visualize alignment using PyMOL in jupyter notebook

[Shenggan]

In my case, you can try to use pymol.cmd.align to do the alignment.

from pymol import cmd
cmd.load('./fastfold.pdb')
cmd.load('./T1024-D1.pdb')
cmd.align('fastfold', 'T1024-D1')

cmd.png('/tmp/foo.png', ray=1)
from IPython.display import Image
Image(filename='/tmp/foo.png')

[mukulem]

Thanks i am able to do this, is there anyway i can rotate this structure?

[Shenggan]

I haven't used a similar function, but refer to pymol's documentation at https://pymolwiki.org/index.php/Rotate