Is Pyrite suitable for small molecules?

Computer-Aided Drug Design at the Durrant Lab Forums Pyrite Is Pyrite suitable for small molecules?

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    • #12471
      Alexandra Tsybizova

      Dear Professor Durrant,
      I was wondering if Pyrite and Blendmol plugins are suitable for the visualization of trajectories of small molecules, like water.

      When I use the example files that are provided with the plugin, everything works fine, however when I try to apply the same procedures to my trajectories, I get the following motion:

      Am i doing it wrong, or is it just the limitation of the software?

      Best regards,

    • #12579
      Jacob Durrant

      Hi Alexandra. Much thanks for your message. Pyrite doesn’t always handle sticks representations well. (Surface and ribbon tend to work better.) But I’ve been able to get it to work with sticks representation using Blender’s Mesh Deform Modifier. First, use BlendMol to separately import both surface- and sticks-representation meshes of the water molecule. Then use Pyrite to drive an animation of the surface mesh. Finally, use the Mesh Deform Modifier to make the surface-representation mesh drive the sticks-representation mesh. It’s a bit convoluted, but I think it should work. Hope this helps!

    • #12619
      Alexandra Tsybizova

      Dear Jacob,
      thank you very much for your answer.
      I tried the things that you suggested, and while they helped to improve the MD visualization, it seems that I still don’t get the correct atomic motion:

      I have also tried similar things on more complicated systems, such as pyridine. There, it seems that the trajectory motion only gets attached to the sticks-representation mesh, while leaving the surface representation unchanged.

      I am puzzled to see where the problem is since it seems that I do everything the same for the water molecule.

    • #12879
      Jacob Durrant

      Hi Alexandra. Much thanks for sending the youtube videos. That’s very helpful. Here are some suggestions:

      1) Remove duplicate vertexes on both the surface and sticks. Pyride includes a "Remove Doubles" option. You can also run "Merge by Distance" in Edit Mode. You might need to run it multiple times until no further

      2) You might try setting up your surface and sticks in VMD. There you can use QuickSurf (instead of Pyrite’s default Surf representation), which is a bit more ordered than Surf. You can save the VMD state as a Visualization State (*.vmd) file, which you can import with BlendMol.

      I put to together a blender file that shows how I did it with a nucleic acid molecule, in case it helps. Here’s the link, which also includes a PDB trajectory and VMD state file:

      You are going to have some distortions in Blender because of the approximations it makes, but you can get pretty close to the original MD simulation. Hope this helps!

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