PyMOL

What PyMOL does

PyMOL is a molecular visualization system that renders three-dimensional molecular and protein structures for scientific research, teaching, and publication. Founded in 2000 by Warren L. DeLano and maintained on an open-source foundation, the product is currently distributed by Schrödinger, which acquired stewardship of the project in 2010 following DeLano's death. The core technology combines Python-based scripting with high-quality ray tracing rendering and runs on Windows, macOS (including Apple Silicon M1–M4), and Linux; add-on modules include AxPyMOL (a Microsoft PowerPoint plugin) and JyMOL (a Java-based development component). A separate PyMOL 2 LTS line is maintained in parallel to the current PyMOL 3.x generation for users prioritizing stability.

The commercial product is sold as annual subscriptions tiered by customer type — Commercial, Government, and Academic/Non-Profit — each with Single User and Tier 1 (lab/department) options, while Tier 2 enterprise licenses (1,000+ employees) are quoted through the Schrödinger Sales Center. Pricing ranges from $99/year (Academic Single User) to $5,250/year (Commercial Tier 1), with multi-year discounts; free Educational builds are available to full-time students and teachers. PyMOL is also distributed open-source via GitHub and conda-forge, and the open-source development is funded by commercial license revenue and the Warren L. DeLano Memorial Fellowship program.

PyMOL's customer base spans universities and non-profit research institutions, pharmaceutical and biotechnology companies, government labs, and the educational community. The product functions as both a standalone revenue-generating line and a flagship open-source brand that anchors user adoption for the broader Schrödinger computational chemistry platform.

Name

PyMOL

Legal name

Schrödinger, LLC

Website

https://pymol.org

Company type

Private

Founded year

2000

Operating status

Operating

Short description

PyMOL is a Schrödinger-maintained, open-source molecular visualization system used by academic, pharmaceutical, biotech, and government researchers — plus students and educators — to render and explore 3D protein and molecular structures for research and publication.

Ownership category

akta.pro rank

Headquarters

HQ city

Mannheim

HQ country

Germany

HQ region

Europe

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

Technology or R&D, Personnel, Operations, Marketing or Sales, Infrastructure

Revenue model

1. Commercial Subscriptions: Annual subscriptions for commercial organizations with Single User (≤25 employees) and Tier 1 (<1,000 employees) license tiers. Includes software upgrades, technical support in English, and access to official documentation.
2. Government Subscriptions: Discounted annual subscriptions for government institutions with Single User and Tier 1 (lab/department) license options. Includes upgrades and support.
3. Academic/Non-Profit Subscriptions: Reduced pricing for academic and non-profit researchers. Single User and Tier 1 (lab/department) options available at significantly lower price points than commercial.
4. Educational Free Access: Free educational-use-only builds for full-time students and teachers for classroom instruction and homework. No obligation for updates, bug fixes, or support.
5. Open Source Sponsorship: Open-source project is funded by commercial license purchases. Sponsors can contribute to the open-source development while using the product.

Pricing tiers

Go-to-market motion3 records

Distribution channels5 records

Marketing channels6 records

Core offering

PyMOL is a molecular visualization system used to render, animate, and explore 3D structures of proteins, small molecules, and chemical complexes for scientific research and education. It is distributed by Schrödinger as a commercial subscription product (PyMOL 3 and PyMOL 2 LTS) alongside a freely available open-source build with permissive licensing, plus targeted offerings including the AxPyMOL PowerPoint plugin, the JyMOL development component, and free Educational-use builds for students and teachers.

Product overview

PyMOL is a molecular visualization system distributed by Schrödinger in both commercial and open-source versions. The current generation is PyMOL 3, with PyMOL 2 LTS (Long-Term Support) also maintained for users preferring stability. The product is available on Windows, macOS, and Linux platforms, and can be installed via conda package manager. Add-on modules include AxPyMOL (PowerPoint plugin) and JyMOL (development component). Schrödinger also provides free Educational-use-only builds for students and teachers. The open-source version is available on GitHub, with most source code freely accessible under a permissive license.

Differentiator

Problem solved

Functional benefit

Brands

• AxPyMOL: Molecular Graphics Plugin for Microsoft PowerPoint
• JyMOL
• Warren L. DeLano Memorial PyMOL Open-Source Fellowship

Products and services

• PyMOL 3 The current-generation PyMOL molecular visualization system for commercial, government, and academic users, offering ray tracing, electrostatics visualization, scene management, and timeline functionality with bundled Python 3.10. Distributed under tiered annual subscriptions (Single User, Tier 1, Tier 2).
• PyMOL 2 LTS Long-term support release of PyMOL 2 maintained for users who prioritize stability over the latest features, including Python 3.11 support. Distributed under the same tiered subscription model as PyMOL 3.
• PyMOL Open-Source Freely available open-source version of PyMOL maintained by Schrödinger, with most of the source code available under a permissive open-source license. Funded by PyMOL commercial license purchases.
• AxPyMOL Microsoft PowerPoint plugin that enables molecular graphics visualization directly within PowerPoint presentations, allowing users to embed and manipulate PyMOL-rendered structures during slide development.
• JyMOL Java-based molecular graphics development component that allows developers to embed PyMOL-style 3D molecular visualization within Java applications.
• Educational PyMOL Free educational-use-only builds of PyMOL available to full-time students and full-time teachers for classroom instruction, homework assignments, and creating figures. Schrödinger has no obligation for updates, bug fixes, documentation, or technical support. Not licensed for academic research or publication.

Segments4 records

Ideal customer profiles4 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Feature6 records

Partnerships

Three partnerships are on record, tiered core and minor.

• SchrödingercoreStrategic or Co-development PartnerSchrödinger maintains and distributes PyMOL as a commercial product while keeping the source code open-source. The company funds open-source development through commercial license revenue and the fellowship program. Warren L. DeLano, the original author, passed away in 2009, and Schrödinger has continued stewardship of the project.
• conda-forgecoreTechnology or IntegrationSince PyMOL 2.5, packages are based on conda-forge. The conda-forge community provides the infrastructure for cross-platform installation of PyMOL alongside Schrödinger-specific channels.
• Warren L. DeLano Memorial Fellowship RecipientsminorStrategic or Co-development PartnerFellowship program awards $12,000/year stipends to open-source contributors including Yuting Chen, Haoling Zhang (2022-2023), Blaine Mooers PhD (2018-2019), Mateusz Bieniek & Paul Smith (2018-2019), and others. Fellows contribute to PyMOL development and community maintenance.

Scale indicators1 record

Recent moves6 records

Expansion highlights5 records

Emerging players

• SAMSON: Software for Adaptive Modeling and Simulation Of Nanosystems, a modular platform for nanoscience modeling with visualization. Comparable as an emerging paid molecular modeling environment positioned as an alternative to PyMOL in research workflows.
• Avogadro: Open-source molecular editor and visualization tool aimed at computational chemists and students. Comparable as a free, extensible viewer/editor with partial overlap to PyMOL, particularly in academic and small-molecule contexts.

Direct peers

• Jmol: Open-source Java-based molecular viewer widely used in education and web-based structural visualization. Comparable to PyMOL's open-source build as a free alternative, particularly in teaching and online publication contexts.
• ICM-Browser: Molsoft's molecular visualization and protein-ligand interaction viewer. Comparable as a paid commercial viewer for drug discovery teams evaluating structural data alongside PyMOL.
• VMD (Visual Molecular Dynamics): University of Illinois molecular visualization tool focused on trajectory analysis and large biomolecular systems. Comparable as a free, cross-platform viewer used by structural biologists and computational chemists, often as a complement or alternative to PyMOL.
• YASARA: Commercial molecular modeling, docking, and visualization program. Comparable as a paid alternative to PyMOL for academic and industrial structural biology and drug design use cases.
• MOE (Molecular Operating Environment): Chemical Computing Group's commercial molecular modeling and visualization suite used in pharma and biotech. Comparable as a paid, cross-platform molecular visualization and drug design platform competing with PyMOL for structural biology and medicinal chemistry workflows.
• UCSF ChimeraX: UCSF-developed molecular visualization program widely used alongside PyMOL in academic structural biology. Directly comparable as a free, cross-platform viewer for proteins and molecular structures with publication-quality rendering.

Broad incumbents

• BIOVIA Discovery Studio: Dassault Systèmes' broad life sciences modeling and simulation suite with molecular visualization capabilities. Comparable as a paid, enterprise-grade alternative to PyMOL for pharma R&D, but spanning a much wider portfolio of modeling tools.
• Schrödinger Maestro: Schrödinger's flagship computational chemistry platform that bundles PyMOL as its visualization component. Comparable as it addresses the same drug discovery customer base but at a much broader scope including molecular modeling, simulation, and predictive chemistry.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks6 records

Key highlights6 records

Customer concentration

• GitHubgithub.com/schrodinger/pymol-open-source
• LinkedInlinkedin.com/company/schr-dinger

Revenue estimate

Valuation estimate

Number of profiles

Funding overview

Funding rounds

Investors

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about PyMOL