Molchanica documentation

Last Updated: April 2026

Introduction

Molchanica is molecule editing, visualization, and dynamics tool with a focus on creating an intuitive user experience. It combines functionality found in PyMol, Chimera, Coot, VMD, GROMACS, and Avogadro, and operates with the focus on visualizing molecules over both time and space. Any molecule you open or build can move using molecular dynamics. We are actively adding work-flow specific functionality; for example, molecular docking, and tools for working with LNPs.

Molchanica includes Computer Aided Drug Design (CADD) tools. For example, molecule screening and generation based on pharmacophores, machine-learning from empirical binding data and more. It automatically estimates ADME and toxicity parameters.

We hope that it's intuitive enough that formal documentation isn't required; installing, running, opening, and viewing molecules should be easy for someone to figure out by downloading, launching, and clicking around the GUI. This documentation is a supplement that experimental process: It describes each feature. It may highlight features you didn't know existed, clarify how to use a given feature, and show assumptions and implementations used.

We've exposed most functionality as top-level UI controls. This improves discoverability, at the cost of adding clutter.

For advanced topics like molecular docking and dynamics, we provide instructions for achieving the best results and displaying assumptions. Use the menu on the left to navigate these documentation pages.

Bottom line: Unleash your inner child: Be fearless, and click things.

Tooltips

Most GUI controls (Text, buttons, input fields, etc) can be hovered over with the mouse to display a tooltip. This text describes what that item does, and hotkeys if applicable.You should be able to discover much of the application's functionality by viewing tooltips for GUI items.

Dive in

If you're new, we recommend that you launch the program, open molecules of interest, and explore the UI at your own pace. Then reference this documentation for help, clarification, and to discover features you weren't aware of. If you don't have a molecule file handy, you may click the "I'm Feeling Lucky" button to open a random protein from RCSB PDB that was uploaded within the past week. Or, experiment with the molecule editor.

Feedback

If you suggestions on how to improve this software, or have a use case we don't support, please send an email, or create an issue on Github.