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CueMol

CueMol is a computer program for the macromolecular structure visualization (CueMol was formerly called "Que"). CueMol's aims are to visualize and create the publication-quality images of the macromolecular structures with user-friendly interfaces. You can find sample images created by CueMol in Gallery page. Currently supported files are molecular coordinates (PDB format), electron density (CCP4, CNS , and MTZ formats), MSMS surface data, and APBS electrostatic potential map (OpenDX format).

Powered by Mozilla XULRunner, the application framework of Firefox and Thunderbird (and other mozilla-based application as well), CueMol2 now runs under both Windows, MacOS X, and Linux in a similar GUI appearance.

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Please send any comments, questions, or requests about CueMol to
mm1mm2 or
Follow @cuemolnohito on Twitter

What's new?

2025/8/14
Released v2.3.0.460. See Releases page for detail.
2025/1/16
Released v2.3.0.454. See Updates page for detail.

Main functions

  • Advanced GUI:

    • Tab-based molecular views
    • Support for multi-molecular scenes
    • Copy&paste of objects (across different scenes)
    • Support for the complete undo/redo operations (with respect to each scene)

  • Supported data formats:

    • Molecular coordinates in PDB
    • Electron density map in X-PLOR/CNS (ascii), CCP4 MTZ and MAP formats
    • Molecular surface (MSMS format)
    • APBS electrostatic potential map (OpenDX format)

  • Store and restore of the scene in XML-based format

  • Supported display:

    • Basic molecular display functions (ball-and-stick model, CPK model, etc)
    • Cartoon model display with tunable interpolation smoothness
    • Edge rendering (with more tunable parameters than PyMOL's one)
    • Solvent-excluded molecular surface (including the generation of the cross-section)
    • Electron density rendering using GPU shader (mesh and volume rendering)
    • Geometric object (solid/dashed lines)

  • Animation functions:

    • Simple spin
    • Camera motion
    • Display fade in/out
    • Structure morphing

  • Inter-operation with external programs

    • Electrostatic potential calculation using APBS and PDB2PQR
    • Rendering using POV-Ray
    • Movie creation using FFmpeg