Guides
Structure Studio and PyMOL
Open PDB entries and AlphaFold models, and change, minimise or dock them by asking, with PyMOL running in your sandbox.
Open a structure
Ask for a structure by PDB ID or by protein name. RBAi searches RCSB PDB when it needs the ID. It fetches the entry from the PDB archive, trying PDBe first and then RCSB, and opens it in the structure viewer. You can also attach your own .pdb file to a message.
AlphaFold models come from the AlphaFold database, with their per-residue confidence (pLDDT) and AlphaMissense pathogenicity scores when you ask for them.
Change it with PyMOL
PyMOL (open source) runs in the code sandbox. A mutation, superposition or edit saves the new structure as a PDB file in the chat’s sandbox, with a download link:
| Ask for | What PyMOL does |
|---|---|
| A mutation | Replaces the side chain with the new residue’s rotamer geometry, not a relabel. |
| A measurement | Atom-to-atom distances, residues within a cutoff of a selection, or a count of matching atoms. |
| A superposition | Aligns two structures and reports the RMSD and the number of aligned atoms. |
| An edit | Several operations in one run: mutate, delete chains or residues, colour by B-factor, show the surface, measure, select nearby residues, align. |
| Your own script | Runs a PyMOL script you write or ask for. |
Note
One PyMOL run can take up to 180 seconds, the sandbox’s limit for a single run.
Structure Studio: edit with AI
Every structure in a chat opens in Structure Studio. Edit with AI, in its top-right corner, opens an assistant under the structure that works with PyMOL in your sandbox; in full screen on a screen 1024 px or wider it opens as a panel beside the structure. It remembers the conversation, so "these residues" refers to what came before.
Ask it to select residues (an interface, a binding site), show them as a surface, sticks or labels, colour by a property, draw hydrogen bonds, salt bridges, hydrophobic contacts, π-stacking or clashes with their counts, or change the structure: mutate a residue, remove a chain, waters, alternate locations or hydrogens, or relieve clashes. For example: show the surface of chain A and the p53 peptide as sticks.
Every change is a new version. Undo, Redo, Download (every version) and Full screen appear beside Edit with AI when you point at the structure or tap it, with the version on screen beside Undo; Ctrl+Z and Ctrl+Shift+Z work too. Display changes are a sentence too: show the ligands, measure the distance between A:Leu54 and B:Phe19, dark background or reset the view.
PyMOL figures, in the studio or in the main chat, are AI-editable: open the figure, describe the change ("label only Trp23", "transparent background") and it is rendered again.
Move, compare and lay out
- Rotate, zoom or spin the view in words:
rotate 90 degrees about y,zoom on the ligand,spin slowly. - Overlay a second structure, for example
overlay 1T4F on this: it is superposed and the answer gives the RMSD. - Side-by-side figures: ask for two views or two structures next to each other.
Minimise and dock
Ask the studio to energy minimise this structure or to dock nutlin-3a into the p53 pocket. The run continues in your sandbox with a progress row and Cancel, and its result is a new version, so Undo returns to the start.
| Run | What it does |
|---|---|
| Energy minimisation | Adds missing atoms and hydrogens (pH 7), then minimises with Amber14 and implicit solvent, heavy atoms gently restrained. Ligands and ions stay in place, and the answer says so. It reports the energies before and after, and how far the structure moved (RMSD). |
| Docking | AutoDock Vina, with the ligand from a name, a SMILES or the one in the structure, and the box around your selection. It returns 9 poses with scores, and the residues within 4 Å of each, with their distances. Scores are estimates, not binding free energies. |
Measured in a real sandbox: minimising PDB 1YCR took 24 s; docking nutlin-3a into MDM2 took 46 s, with the best pose (−7.2 kcal/mol) in the p53 pocket. Molecular dynamics and structure prediction run from the main chat.