Try this

while exporting an isosurface as an .stl mesh object, the resulting file typically does not contain explicit information about the original coordinates and scale of the system. This is because .stl files primarily store the geometry of the mesh, such as vertices and faces, rather than the absolute coordinates.

1. Before exporting the isosurface to .stl, make note of the original coordinates and scale of the system in your code or documentation.

2. Export the isosurface as an .stl file using the tools or libraries available to you. This will give you a mesh representation of the surface.

3. After exporting the mesh, create a separate text file (let's call it "coordinates.txt") where you store the original coordinates of the points in the isosurface. Each line of the file should contain the XYZ coordinates of a point, corresponding to the vertices of the mesh.

4. When you parse the .stl file and extract the cloud of points, match each point with its corresponding XYZ coordinates from the "coordinates.txt" file. This way, you can associate the original coordinates with the vertices of the mesh.

5. Use the matched coordinates to create a pseudo-pdb file. The pseudo-pdb file should contain the XYZ coordinates in the same format as a standard PDB file. You can use a text editor or a scripting language to generate the pseudo-pdb file based on the matched coordinates.

6. Load the pseudo-pdb file into VMD, which should now contain the original coordinates and scale of the system. You can calculate distances to a molecule using the pseudo-pdb file as you intended.

By storing the original coordinates separately and associating them with the mesh vertices, you can preserve the coordinate information even though it's not directly encoded in the .stl file.

Good luck

To export an .stl file on VMD while keeping the original coordinates, you can use the following steps:

Thank you for your replies Mohammad Imam and Chuck A Arize .

After playing around with VMD options and the Tk console I managed to get what I needed. For anyone that might face this same issue (since documentation is quite poor in this matter), what I did is the following:

1) Load the cube (or any surface object you might want to export) into VMD and set the representation to Isosurface with the desired isovalue and style (I use Draw: Wireframe and Show: Isosurface).

2) Within the tk console, create a variable containing the identity matrix and use it to set the transformation matrices to it:

set id_matrix {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}

molinfo top set center_matrix [list $id_matrix]

molinfo top set rotate_matrix [list $id_matrix]

molinfo top set scale_matrix [list $id_matrix]

NOTE: This will move the scene and likely leave the object out of view if it was not originally in 0,0,0. It is important to not move the camera or modify the view at all from now on, since that would alter the transformation matrices we just set.

3) Now we can go to File > Render... and select STL. This will export the triangle mesh object with the correct positioning within the global space.

From here, you can use any parser to extract the xyz coordinates of the vertices of the triangles forming the mesh, also taking care of duplicate points, since triangles overlap and that can increase the size of the files up to 3 times.

I used the stl python module to extract a list of points and then made a python script to write a PDB file containing pseudo atoms (DUM) with those coordinates. This file can then be loaded into VMD and it will overlap with the original isosurface.

I hope this helps anyone that might be stuck in a similar situation.

Cheers.