How to transform a surface to match original pdb reference frame

[OliviaViessmann]

Describe the bug I am using create_mesh() to generate surfaces. The background pymol commands generates an .obj which contains the vertices and faces, but it centers the protein, so the original pdb coordinates and the mesh do not align. How can I transform the surface vertices to match the original pdb reference frame? After reading about the specific order of rotations and translations in pymol I adapted the get_obj_file() in graphein using a transformation command from the pymol Q&A before the .obj file is saved, but it doesn't do anything. I call the lines below after pymol.load(pdb_file) and before pymol.save

view = list(pymol.get_view())
M = view[0:3] + [-view[12]] + view[3:6] + [-view[13]] + view[6:9] + [-view[14]] + view[12:15] + [1.0]
pymol.transform_selection("(all)", M, 0, 0, 0, 1)
pymol.set_view([1, 0, 0, 0, 1, 0, 0, 0, 1] + view[9:])

Expected behavior Does anyone have any ideas how I can align the pdb residue coordinates and the graphein vertex coordinates?

[a-r-j]

It appears you need to reset the camera view. Can you try this config? It works for me.

import graphein.protein as gp

config = gp.ProteinMeshConfig(pymol_commands=["show surface", "set_view (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, -50.0, 0.0, 0.0, 0.0, 40.0, 100.0, -20.0)"])```

[OliviaViessmann]

Cool, this indeed resets it! A question -- how did you chose the values for the matrix? Are these the defaults for the original view? Thanks a again for the help!

[a-r-j]

They came to me in a dream :)