Show the interaction you actually calculated
To make a useful binding-site figure in ChimeraX, choose one ligand and one protein copy, calculate hydrogen bonds separately from general contacts, then show only the surrounding atoms needed to explain the result. Keep the calculation settings with the image. A short distance is a geometric observation; it does not, by itself, identify a hydrogen bond, measure binding strength or establish why a drug works.
This workflow uses the human Abl kinase domain with imatinib in PDB entry 2HYY. You will create three distinct outputs: a hydrogen-bond candidate list, a contact list and a distance-only neighbor list. The final figure should make clear which calculation supplied its lines.
The four illustrations here are conceptual CGI, not renderings of 2HYY or evidence for any atom pair. For broader composition advice, see the existing protein-ligand visualization guide. Here the added task is an auditable calculation and figure procedure.
Start with a known structure and version
Install UCSF ChimeraX and open a fresh session with no other molecular models. Make an empty working folder for the session and text outputs. Use File > Set Working Folder, or the cd command with a quoted absolute folder path, before running commands that save relative filenames.
We executed the loading, display commands, interaction calculations, distance measurement and session save in ChimeraX 1.9 on Windows. We checked the procedure against the official documentation available on October 12, 2026. Interactive camera framing and PNG export below are documented steps, not a claimed local render test.
The RCSB record for 2HYY identifies an X-ray structure at 2.40 Å resolution, with protein chains A through D and ligand code STI. An ångström, written Å, is one ten-billionth of a meter. Keep the entry identifier, downloaded coordinates and software version with your output; resolution is not an error bar for every measured atom distance.
Choose one protein-ligand copy
Run “open 2hyy”. In a fresh session this becomes model #1. Inspect the Log and Model Panel before continuing. Our example uses chain A and its STI residue, numbered 600 in the loaded structure. The full entry contains multiple copies, so an unqualified :STI selection would include more than the intended ligand.
Run “hide #1 atoms”, then “hide #1 cartoons”, then “show #1/A cartoons”. Show the selected ligand with “show #1/A:STI atoms” and use “style #1/A:STI stick”. These commands change display; they do not delete the other copies from the coordinates.
The atom specification #1/A:STI means model 1, chain A, residue name STI. Keep that scope in every calculation. The other selection, (#1/A & protein), means the protein atoms of chain A. Water and the ligand itself are outside that protein-only set.
RCSB also provides biological assemblies for this entry. This procedure intentionally uses the author chain identifiers in the opened entry rather than generating another model. If your scientific question depends on an interface between subunits, choose the assembly first using the biological-assembly guide; do not silently discard the interacting partner.
Calculate hydrogen-bond candidates
Run “cartoon suppress false” so backbone atoms can be shown alongside the ribbon. Then run “hbonds #1/A:STI restrict (#1/A & protein) relax true distSlop 0.4 angleSlop 20 reveal true log true saveFile hbonds.txt”.
The hbonds command uses chemical atom types and geometric criteria. Here we explicitly allow the documented distance and angle tolerances: 0.4 Å and 20 degrees. The reveal option displays relevant atoms; the text file preserves donor, acceptor and distance information.
Our protein-only calculation returned four candidates. For example, the backbone nitrogen of Met318 and ligand atom N3 had a donor-to-acceptor distance of approximately 2.94 Å. The file records 2.937 Å, but extra displayed decimals do not establish equivalent physical precision.
The deposited example has no explicit hydrogens for these pairs. ChimeraX uses inferred geometry where appropriate. Describe the output as geometrically identified hydrogen-bond candidates under stated settings. The documented algorithm can report alternatives that could not all coexist; its count is not a measurement of simultaneous bonds in solution.
Calculate broader contacts separately
Run “contacts #1/A:STI restrict (#1/A & protein) overlapCutoff -0.4 hbondAllowance 0 makePseudobonds false reveal true log true saveFile contacts.txt”.
ChimeraX defines overlap using the two atoms’ van der Waals radii minus their separation, with an optional hydrogen-bond allowance. Van der Waals radii describe effective atomic sizes in this geometric test. A negative overlap threshold includes atoms separated slightly beyond the sum of those radii.
The contacts documentation explains that the search includes polar, nonpolar, favorable and unfavorable contacts. It is not a binding-energy calculation. We explicitly set the threshold and allowance because software versions can differ in defaults.
With these settings, our local example returned 86 atomic contacts. That means atom pairs, not 86 distinct residues or 86 stabilizing bonds. The makePseudobonds false option keeps this larger set out of the picture while reveal true exposes the surrounding residues for inspection.
Use a distance cutoff for a different question
If the question is simply which protein atoms lie within a chosen radius of the ligand atoms, run “contacts #1/A:STI restrict (#1/A & protein) distanceOnly 4 makePseudobonds false log true saveFile neighbors-4A.txt”.
This substitutes a center-to-center cutoff of 4 Å for the overlap criterion. Our local example returned 112 atom pairs. Four ångströms is an illustrative neighborhood choice here, not a universal definition of an interaction or an optimized scientific threshold.
Do not compare 112 with 86 as if one run discovered additional experimentally confirmed bonds. The queries answer different questions. Keep the outputs in separate files, and choose the one that matches the statement your figure needs to support.
| Output | Criterion | What the count means |
|---|---|---|
| hbonds.txt | Atom types and relaxed geometric criteria | 4 candidate hydrogen bonds in this run |
| contacts.txt | VDW overlap at least -0.4 Å; allowance 0 | 86 qualifying atomic contacts |
| neighbors-4A.txt | Atomic centers at most 4 Å apart | 112 distance-qualified atom pairs |
Measure one pair and frame the pocket
To inspect the Met318 example directly, run “distance #1/A:318@N #1/A:600@N3”. Save the measurements with “distance save distances.txt”. The distance command creates a monitor between those atom centers; it does not classify the interaction chemistry.
For the visible figure, rotate the structure until the ligand and the relevant sidechains are separated in projection. Use “view #1/A:STI clip false” as a starting point, then zoom out enough to include every endpoint and residue label you need. Framing is an interactive step, so inspect the actual output rather than assuming the first view is usable.
Keep a ribbon segment or another clear orientation cue. If a line disappears, verify that both endpoint atoms are displayed. A hidden endpoint can hide its pseudobond, and ribbon display can obscure backbone atoms unless simultaneous display has been enabled.
Choose either the hydrogen-bond overlay or a small, explicitly identified distance measurement set for the final panel. Several overlapping dashed lines in different categories are difficult to interpret even when each calculation is correct.
Save the figure with its audit record
Run “save binding-site.cxs” to preserve the session. After completing the view in the graphical application, use “save binding-site.png width 2400 height 1800 supersample 3”. These image dimensions are an illustrative output choice, not a journal requirement. Recheck framing in the saved PNG because its aspect ratio may differ from your working window.
The save documentation describes image dimensions, supersampling and session files. For an overlay on a slide, the separate transparent-background guide explains the alpha-channel option. Keep an opaque preview too so pale lines can be reviewed easily.
Package the coordinate file, command record, software version, three calculation files, distance file, session and final image together. A collaborator should be able to identify the modeled atoms and selection scope without reverse-engineering the colors in a screenshot.
- Confirm model #1, author chain A, ligand STI600 and the coordinate source.
- Record whether waters, other chains and explicit hydrogens were included.
- Record overlap, allowance, distance cutoff and hydrogen-bond tolerances separately.
- Check endpoint visibility and label legibility at the final printed or displayed size.
Write a caption that matches the calculation
A reusable caption draft is: “Binding-site view of imatinib in the Abl kinase domain, based on PDB 2HYY, author chain A. Dashed lines indicate ChimeraX hydrogen-bond candidates with distance and angle tolerances of 0.4 Å and 20 degrees. Calculations were restricted to STI600 and chain-A protein atoms; waters were excluded. The Met318 N to STI600 N3 distance is approximately 2.94 Å.”
Use that text only if your final panel actually retains that overlay and measurement. Add your software version and explain any omitted labels, changes to coordinates or alternative atom locations. If the image shows only general contacts, replace the hydrogen-bond wording with the exact contact criterion.
Avoid claims about drug potency, residence time or a binding pathway from this static picture alone. A deposited pose and a geometric analysis can support a structural explanation, but those other claims need appropriate experiments or validated calculations. The attractive CGI illustrations in this article do not supply that missing evidence.
Fix the common mismatches
When a result differs, compare inputs and settings before editing the image to match an expected number. The official UCSF tutorial examines a generated assembly and permits interactions beyond our protein-only scope. Its totals are therefore not interchangeable with the explicitly scoped results above.
Do not delete waters just to obtain a cleaner count. Excluding them is a declared choice in this example. For a question about water-mediated interactions, keep the relevant waters, evaluate their structural support and calculate that separately.
| Problem | Check | Correction |
|---|---|---|
| Many copies appear | Model and chain scope | Use #1/A:STI; inspect the opened model before running |
| A dashed line ends at a ribbon | Backbone display and endpoint visibility | Use cartoon suppress false and reveal true |
| Contact counts differ | Version, allowance and atom selections | Use explicit settings and compare saved text files |
| Nearby pairs are called hydrogen bonds | Which command generated the list | Use hbonds for its chemical and geometric classification |
| Image differs from the session view | Output aspect ratio and hidden overlays | Open the actual PNG and inspect every label |
FAQ
Are all ChimeraX ligand contacts hydrogen bonds?
No. The contact search uses an overlap or distance criterion and can include different kinds of close approach. Use the hydrogen-bond calculation and report its chemical assumptions and tolerances separately.
Why does this example find four hydrogen-bond candidates?
It restricts the search to one STI ligand and chain-A protein atoms in 2HYY. Water and other copies are excluded. Different coordinates, selections or settings can change the result.
Does a 4 Å distance cutoff measure binding strength?
No. It identifies atom pairs within that center-to-center distance. It does not calculate affinity, interaction energy or the probability that a contact persists in solution.
Should I add hydrogens before running the tutorial?
This example deliberately uses the deposited input without adding them. ChimeraX can infer positions for its analysis; adding hydrogens introduces protonation and orientation choices that should be recorded and reviewed.
Can I turn this figure into an animation?
Yes, but preserve the distinction between a camera move around a static structure and a biological transition. A plausible-looking ligand approach is not a measured binding pathway.
Try a conceptual binding explanation
Use the coordinate-derived ChimeraX figure when the reader needs to inspect particular atom pairs. For a broader teaching scene, try Animiotics with a brief such as: “Show a small ligand beside a protein pocket, move the camera to reveal the pocket opening, then hold on the bound state. Keep the approach explicitly conceptual and do not display measured distances or binding energies.” This is a proposed brief, not a tested simulation or a guarantee of a particular result.
The current Animiotics workflow lets you describe a scientific scene and edit its camera, colors and timing. Review the resulting geometry and explanation against your source figure. Sign-up and the manual editor are free; AI generation and exports require a paid plan.