PyMOL Alternatives

PyMOL is described as 'Powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures' and is an app in the education & reference category. There are more than 10 alternatives to PyMOL for a variety of platforms, including Mac, Windows, Linux, Web-based and Android apps. The best PyMOL alternative is Avogadro, which is both free and Open Source. Other great apps like PyMOL are Calistry.org, UCSF Chimera, Jmol and Rasmol.

PyMOL iconPyMOL
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PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures.

More about PyMOL
More about PyMOL
PyMOL alternatives page was last updated Dec 2, 2024
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  1. Avogadro icon
    Avogadro icon

    Avogadro

     15 likes
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    Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

    21 Avogadro alternatives
    A simple molecule in a small Avogadro window.

    License model

    • Free • Open Source

    Platforms

    • Mac
    • Windows
    • Linux
    Viewing a slightly more complex molecule, vemurafenib.
    Avogadro iconPyMOL Icon

    Avogadro VS PyMOL

    Is Avogadro a good alternative to PyMOL?
     

    • Avogadro is the most popular Windows, Mac & Linux alternative to PyMOL.

    • Avogadro is the most popular Open Source & free alternative to PyMOL.

    • Avogadro is Free and Open SourcePyMOL is Paid and Open Source
  2. Calistry.org icon
    Calistry.org icon

    Calistry.org

     6 likes
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    Calistry is an online Chemistry Calculator. Till date Calistry contains 70+ calculators in the field of Chemistry. Everything in the website is entirely free to use. Other than calculators, Calistry also provides online molecular viewers that visualizes coordinate file of...

    13 Calistry.org alternatives
    Calistry.org

    License model

    • Free • Proprietary

    Application type

    Platforms

    • Online
    • Android
    GROMACS gro/LAMMPS dump file online visualiser.
    Calistry.org screenshot 2
    Calistry.org iconPyMOL Icon

    Calistry.org VS PyMOL

    Is Calistry.org a good alternative to PyMOL?
     

    • Calistry.org is the most popular Web-based & Android alternative to PyMOL.

    • Calistry.org is Free and ProprietaryPyMOL is Paid and Open Source
  4. UCSF Chimera icon
    UCSF Chimera icon

    UCSF Chimera

     2 likes
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    UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data.

    8 UCSF Chimera alternatives

    License model

    • Free • Proprietary

    Platforms

    • Mac
    • Windows
    • Linux
    UCSF Chimera iconPyMOL Icon

    UCSF Chimera VS PyMOL

    Is UCSF Chimera a good alternative to PyMOL?
     
  5. Jmol icon
    Jmol icon

    Jmol

     3 likes
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    Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

    11 Jmol alternatives
    Acetic acid using CPK colors and spacefilled atoms.

    License model

    • Free • Open Source

    Platforms

    • Mac
    • Windows
    • Linux
    Display of bounding box and axes of coordinates space. Note the transparency of the yellow halo around selected atoms.
    The electrostatic potential of allene mapped onto a translucent surface
    +2
    An SN2 reaction animation with the distance measured between the chlorine and carbon atoms
    Jmol iconPyMOL Icon

    Jmol VS PyMOL

    Is Jmol a good alternative to PyMOL?
     
  6. Rasmol icon
    Rasmol icon

    Rasmol

     2 likes
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    RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank.

    13 Rasmol alternatives
    Image export options
    Protein viewed as cartoon

    License model

    • Free • Open Source

    Platforms

    • Mac
    • Windows
    • Linux
    Rasmol iconPyMOL Icon

    Rasmol VS PyMOL

    Is Rasmol a good alternative to PyMOL?
     
  7. QuteMol icon
    QuteMol icon

    QuteMol

     1 like
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    QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects.

    6 QuteMol alternatives
    QuteMol screenshot 1

    License model

    • Free • Proprietary

    Platforms

    • Mac
    • Windows
    QuteMol screenshot 1
    QuteMol screenshot 2
    +1
    QuteMol screenshot 3
    QuteMol iconPyMOL Icon

    QuteMol VS PyMOL

    Is QuteMol a good alternative to PyMOL?
     
  9. VMD - Visual Molecular Dynamics icon
    VMD - Visual Molecular Dynamics icon

    VMD - Visual Molecular Dynamics

     1 like
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    VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

    7 VMD - Visual Molecular Dynamics alternatives
    VMD - Visual Molecular Dynamics screenshot 1

    License model

    • Free • Open Source

    Platforms

    • Mac
    • Windows
    • Linux
    VMD - Visual Molecular Dynamics screenshot 1
    VMD - Visual Molecular Dynamics screenshot 2
    VMD - Visual Molecular Dynamics iconPyMOL Icon

    VMD - Visual Molecular Dynamics VS PyMOL

    Is this a good alternative to PyMOL?
     
  10. ChimeraX icon
    ChimeraX icon

    ChimeraX

     1 like
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    UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and...

    5 ChimeraX alternatives

    License model

    • Free Personal • Proprietary

    Platforms

    • Mac
    • Windows
    • Linux
    ChimeraX iconPyMOL Icon

    ChimeraX VS PyMOL

    Is ChimeraX a good alternative to PyMOL?
     
  11. RasTop icon
    RasTop icon

    RasTop

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    RasTop is a molecular visualization software adapted from the program RasMol, which was initially developed by Roger Sayle. RasTop is particularly adapted for educational purposes and for the rapid analysis of macromolecules at the bench.

    11 RasTop alternatives
    RasTop screenshot 1

    License model

    • Free • Open Source

    Platforms

    • Mac
    • Windows
    • Linux
    • Wine

    RasTop Features

    1.  Rendering
    RasTop iconPyMOL Icon

    RasTop VS PyMOL

    Is RasTop a good alternative to PyMOL?
     
  12. Vipster icon
    Vipster icon

    Vipster

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    Vipster is a powerful and versatile tool for pre- and post-processing of periodic chemical structures. It's designed from the ground up with periodic simulations in mind.

    10 Vipster alternatives
    Vipster screenshot 1

    License model

    • Free • Open Source

    Platforms

    • Linux
    • Flathub
    • Flatpak
    • Windows
    • Mac
    • Self-Hosted

    Properties

    1.  Privacy focused

    Features

    1.  Works Offline
    2.  Ad-free
    3.  No Tracking
    4.  No registration required
    Vipster iconPyMOL Icon

    Vipster VS PyMOL

    Is Vipster a good alternative to PyMOL?
     

    • Vipster is the most popular Self-Hosted alternative to PyMOL.

    • Vipster is Free and Open SourcePyMOL is Paid and Open Source
    • Vipster is Privacy focusedPyMOL is not according to our users
10 of 10 PyMOL alternatives