Create or delete specific bond between two specific atoms

[davidkastner]

Hi! Anyone know how to add or delete specific bonds between specific atoms? I am trying to render a chemical reaction for a metalloprotein with a Fe residue from a QM calculation. So far it is working great but I want to create bonds between the iron atom and the coordinating atoms. Since coordinating dative bonds are quite long (2 to 3 angstroms), I can't use the topology find bonds node without ending up with a lot of noisey bonds everywhere. I also have a bond that forms from an unusually short hydrogen bond from the QM calculations, which would be nice to delete. I don't see a selection node to select two specific atoms in a single bond.

For example, the iron has a Res Name of FE and an Atom ID of 763. One of the coordinating atoms is from an Glu oxygen with an Atom ID 65 and an Atom Name O7. The atom names are a little odd since they came from an XYZ from a QM calculation but every atom has a unique Atom ID and Atom Name.

[BradyAJohnston]

Unfortunately in Geometry Nodes it's still quite difficult to create a single edge between vertices (what MN uses as bonds). Is this a trajectory or a static structure? If static then you could manually create bonds by selecting two vertices while in edit mode of the mesh & pressing the F key to create an edge / bond between them. You could also manually delete edges as well this same way, by selecting both vertices or the edge and pressing x to dissolve / delete edges. Better edge creation and deletion is currently limited by Geometry Nodes as far as I've been able to figure out.

[davidkastner]

Thanks for the ideas! This is a PDB trajectory so an ensemble of separate MODEL entries. Since it is a QM trajectory there are only 600 frames but that is probably still too many to edit manually. While I had my fingers crossed for an easy fix I was missing, I've been brainstorming some ideas that could work.

For example, break the trajectory into three pieces and load them in together as separate MN objects. One trajectory would be all atoms except iron and the problematic tyrosine with the short Hbond. The second would be Iron plus only a single atom from each coordinating residue that way I can select single atoms as residues as each coordinating "residue" will now be a single atom. And the third would be just the problematic tyrosine. Since it will now be separate it should not identify an hydrogen bond. It's a little messy but I think it might work.

[BradyAJohnston]

Are the bonds changing between frames of the trajectory? You could create a single structure which is static, manually tweak the bonds, then just sample the positions from the animated trajectory to change the positions of the structure with the edited bonds.

[davidkastner]

There are bonds forming and breaking across the course of the reaction as the substrate degrades. However, the coordinating bonds remain constant.

[BradyAJohnston]

Hmm this is a tough one. I think probably your approach of doing a separate object for each subset might be the best approach. If you duplicate the objects with Alt + D instead of Shift + D then they will share the same underlying mesh data which will get updated, rather than having to import the trajectory multiple times.

[davidkastner]

Oh interesting! Are you saying that there is a way to delete atoms in MN objects? I was going to preprocess the trajectories such that when I loaded them into Blender they would already only be the specific atoms that I needed for the bonds. You are thinking I could load in one trajectory with all the atoms, make three copies, and then modify the different copies to only include the atoms that I am interested in?