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Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...

Fischer Projections

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines.

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Related Experiment Video

Updated: Jun 25, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware

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Published on: December 25, 2021

CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer.

David Meijer¹, Marnix H Medema², Justin J J van der Hooft³

¹Bioinformatics Group, Wageningen University & Research, Wageningen, the Netherlands. david.meijer@wur.nl.

Journal of Cheminformatics

|May 24, 2024

Summary

CineMol generates 2D Scalable Vector Graphics (SVG) visualizations from 3D small molecule models quickly and efficiently. This Python-based tool enhances cheminformatics research with accessible, customizable molecular graphics for publications.

Keywords:

Molecular drawing Scalable vector graphics Three-dimensional structure Visualization

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Area of Science:

Cheminformatics
Computational Chemistry
Scientific Visualization

Background:

Effective visualization of small molecules is crucial in cheminformatics for conveying complex data and results.
Scalable Vector Graphics (SVG) are ideal for molecular visualizations due to their scalability and post-production editability.
Existing software often lacks direct SVG output from 3D models and programmatic Python accessibility.

Purpose of the Study:

Introduce CineMol, a novel Python-based tool for generating 2D SVG visualizations of 3D small molecule models.
Address the need for efficient, programmatically accessible SVG generation in cheminformatics workflows.
Provide researchers with a tool for creating customizable and publication-ready molecular graphics.

Main Methods:

CineMol generates vectorized approximations of 3D small molecule models directly into SVG format.
The process avoids computationally intensive methods like triangulation or ray tracing, ensuring speed.
The tool is written in Python, relying only on native libraries for broad compatibility.

Main Results:

CineMol produces SVG files rapidly (seconds) with small file sizes (50-300 KB for up to 45 heavy atoms).
Output SVGs are easily editable in standard vector graphics software.
The tool offers programmatic control over per-atom and per-bond visualization parameters.

Conclusions:

CineMol provides a fast, efficient, and accessible solution for generating 2D SVG molecular visualizations from 3D models.
Its Python integration and customization capabilities make it a valuable asset for cheminformatics, metabolomics, and related fields.
CineMol enhances the visual impact and clarity of scientific communication in molecular research.