World coordinates of generated objects do not match PDB file

Computer-Aided Drug Design at the Durrant Lab Forums BlendMol World coordinates of generated objects do not match PDB file

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    • #28109

      Hello, I have a very simple use case I am trying to solve. I have a .ply (or could be another mesh format) file that represents the surface of a protein, which is generated from a protein structure by another program. The coordinates of this mesh are the same coordinate frame as that of the PDB file which contains the protein structure.

      I import this mesh into blender, and then use your plugin to generate a cartoon or stick representation of the protein which I want to use in conjunction with the mesh I already have – however these do not align. They are not in the same coordinate frame, or even the same scale. It appears BlendMol performs some transformation on the object coordinates?

      Is there some way to rectify this?

    • #37841
      Jacob Durrant

      Hi Jared. Much thanks for your question, and sorry for my delayed response. BlendMol is actually specifically designed not to change the coordinate frame. In my experience, many other ways of exporting molecular meshes do recenter the protein before export. I suspect whatever program you’re using to generate the ply file is the one that’s resetting the frame. Hope this answer helps. Take care.

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