About Visualization

[Angenb]

I am highly interested in the prediction of protein conformations within this project. I recently attempted the prediction of adenosine kinase and obtained a pdb file along with two npz format files. I wish to visualize these results as demonstrated on your website but am uncertain about which tools to use. Could you please provide information on the software and tools required for visualization and the steps involved? This assistance would be greatly appreciated. Thank you.

[dcbiton]

Hi @Angenb , I am not from the microsoft team but you can visualize the pdb files using visualization apps (example: namd, chimera, etc) but if you are using python, you can use biopython with nglview
example:

from Bio.PDB import (
    PDBParser
)
import nglview as nv # visualizing
parser = PDBParser()
filename = 'output_filename.pdb'
structure = parser.get_structure("protein", filename) 

view = nv.show_biopython(structure)
view

I hope this helps