LOAD A PDB FILE

Setup

  • Blender version 4.0
  • Blender empty file

PDB MOLECULE

Got a structure of ciprofloxacin in SDF format from here:

https://www.molinstincts.com/sdf-mol-file/ciprofloxacin-sdf-CT1000048109.html

translated to PDB with:

https://datascience.unm.edu/tomcat/biocomp/convert (3D)

Sometimes you get DivisionByZero, try to use a different converter.

WORKFLOW

  1. Delete the cube with X

  2. Import file Ciprofloxacin

  3. Import Settings:

    Parameter Value
    Balls type Mesh
    Balls radius 0.5
    Stick type Duplivert
    Bonds Active
    Bond radius 0.1
  4. Now we are going to merge all atoms and sticks to create a unique mesh. We will work in the Outlier
  5. Select Hydrogen and hide it, notice that the sticks are closed.
  6. Remove the cups just deleting the underling model (Hydrogen_sticks_cup)
  7. Do the same for all sticks: extra faces will interfere with shading.
  8. Convert the instance of Carbon_Stick_mesh to a real mesh: CTRL-A and make instance real.
  9. Select an active stick with CTRL-Click and CTRL-J to join segments
  10. TAB to enter edit mode and than M and merge by distance to cleanup vertices
  11. Do this tedious thing for all the sticks, remember to go back in object mode.
  12. Join all sticks in a single mesh: select in outlier and CTRL-J and rename it sticks
  13. On Outlier, create a new collection under Scene collection (name: ‘Molecule’)
  14. In Outlier move the sticks object to the new collection
  15. Do the same with atoms:
    • CTRL-A make instance real
    • CTRL-Click and select one atom
    • CTRL-J and join all
    • TAB and M to merge by distance
  16. Merge all atoms together with CRTL-J
  17. Named it balls and move to the collection Molecule
  18. Select balls: In the Material properties you notice there are multiple materials: rename them as XXX.Atoms (example: Carbon.Atoms)
  19. Now we want to separate the bonds and atoms materials. Select sticks and make new materials called XXX.Bonds
  20. We can now merge sticks and balls with CTRL-J
  21. Rename final mesh Ciprofloxacin
  22. Now that we have a single molecule we can do a lot of cool things! For example let’s WAVE this molecule for no reason!
  23. On Modifiers add a Wave modifier, play animation and see your molecule waving!
  24. Add a rotating animation:
    • Remove the wave
    • N for item properties
    • I overing ‘Rotation’ to insert a keyframe
    • Go to frame 100
    • Rotate 360 on Z axis with RZ360
    • Go to frame 120
    • Rotate again on Z axis 360
  25. Render animation (EEVE)

Blender file: 02_fix_pdb_complete.blend