Every structure has a shape worth getting right.

01Interface

CYLview was designed and optimized for experimental chemists who want to use computational chemistry as a practical tool, not a specialty in itself. Other programs offer similar functionality, but are often technically demanding to master — CYLview asks for a minimum of computer knowledge to get structural insight out of a calculation.

Written in Python, it's fully portable across Windows, macOS and Linux. Every tool lives inside the same window — lighting, scenes, and analysis each get their own tab rather than a separate program — including an integrated file browser that lets you move through a large batch of files the way you'd browse database entries. CYLview quietly saves each file's orientation and settings as you go, so re-inspecting a set of structures stays fast.

02Presentation styles

A wide range of visual styles are available to suit different kinds of molecules — including the Houkmol style, used internally in the Houk group for the past fifteen years. It's built specifically so atoms and bonds stay distinguishable even in black-and-white printouts, which makes it well suited to publication.

Eight bond styles cover different molecular states — dynamic, double/triple, partial, aromatic and haptic among them — assigned automatically from hybridization and ring perception, with hapticity detected on its own. A dynamic TS bond style shows bonds changing along a reaction pathway (IRC) or a molecular dynamics trajectory.

03Rendering & lighting

Surfaces and highlights render cleanly even where several overlap, with up to three lights — each independently colored and positioned, with optional shadow mapping — set from a dedicated Lights tab. Molecular orbital surfaces get live opacity and material editing, alongside VdW, SAS and highlight surfaces and ORTEP-style displacement ellipsoids.

For depth, fog is the common cue; focal blur is rarer in molecular visualization but effective for a different reason — it naturally draws the eye to whatever's in focus, and can now follow a selected atom. Both are fully customizable, with intensity and depth you adjust by hand.

04Animations

Even with these tools, a single image can't always capture a complex structure — and stringing together snapshots forces the viewer to mentally reorient the molecule between frames. CYLview's animation module solves this directly: choose the orientations you want, and CYLview interpolates every frame between them into a smooth, continuous movie — with bounce, warp, and fade-in modes for how it plays. No technical knowledge of animation required.

Vibrational frequencies animate the same way, with a frame slider and direct movie export.

05Textual information

Select a pair of atoms and CYLview adds a distance label automatically, with adjustable precision and optional units. Angle arcs and label tethers illustrate relationships directly on the structure, and update automatically as you move or rotate it — the tether threshold is adjustable too, and labels place themselves to stay legible as the structure moves. For more flexibility, custom labels can be linked to a single atom, with basic subscript and superscript support. CYLview also includes a function to rapidly generate Newman projections, essential for depicting and comparing structures.

06Interaction analysis

Understanding a computed structure means quickly seeing how many interactions it has, where, and how strong. As soon as a 3D structure file is read, CYLview generates a list of every pair of elements in steric contact. The vdW module lets you examine those contacts by element pair and by strength threshold — set as a % of the sum of van der Waals radii — adjustable on the fly, then select and label the contacts you want for a publication-quality representation.

07Analysis & parsers

CYLview reads XYZ, Gaussian, and ORCA output natively, evaluating geometry optimization and frequency jobs quickly and directly — including ORCA thermochemistry, IRC pathways, NBO, and natural population analysis. A dedicated workflow handles conformers: RMSD analysis, clustering, and auto-alignment across a full set at once.