New Features

PyMOL 1.8

Open Source and Incentive

  • changed defaults:
    • ignore_case=off. This has major implications for all scripts which are agnostic about identifier case in selection expressions. E.g. "select foo, chain a" won’t work for chain A.
    • fetch by default downloads mmCIF files (type=cif)
    • scene_buttons=on
  • finalize CIF/mmCIF support:
    • add support for discrete=1 loading of CIF files
    • improve multi-model loading (inhomogenious models, pdb_honor_model_number support)
    • support loading multiple objects ("data_" blocks) from one CIF file (multiplex != 0)
    • set cartoon_trace_atoms and ribbon_trace_atoms for CA-only models
    • assembly setting: load biological unit
    • Ignore "auth" identifiers with cif_use_auth=off (default: on)
    • Display full sequence (incl. missing residues) with cif_use_auth=off (uses _entity_poly_seq)
    • Bundled components dictionary subset for connect_mode=4
  • added file types support: pdbqt, pdbml, cml
  • API: cmd.get_object_ttt()
  • Tcl/Tk window:
    • Simple font size dialog (Setting > GUI Font Size)
    • Feedback when changing settings
  • support cartoon_trace_atoms for beta-sheets

Incentive Only

  • improved mae support
  • render zero-order bonds as dashed lines or sticks
  • A > compute > surface area > per residue (get_sasa_relative)
  • fixes stick and sphere rendering issues on OS X with ATI Radeon R9 graphics cards

    PyMOL 1.7.6

    Incentive Only



      • Order independent transparency for real-time rendering (transparency_mode=3)
      • chromadepth
      • Experimental Retina resolution support in MacPyMOL (--retina command line flag)

      Open Source and Incentive

      • expose "reps" and "protons" to iterate/alter

      PyMOL 1.7.4

      Open Source and Incentive

      • faster mmCIF loading
      • multi-letter chain support
      • connect_mode=4
      • added file types support: idx, spi

      Incentive Only

        • cartoon transparency, sorted in real-time

        PyMOL v1.7.2 (Release Date: August 4, 2014)

        Incentive Only

        • Pre-integrated volume rendering: Reduces layering artefacts in volumes. It's the new default for volume objects in Incentive PyMOL.

          volume_mode=1 (default)
        • Real-time antialiasing: Antialiasing was so far a ray-tracing-only feature. Now real-time graphics also supports antialiasing, it's disabled by default and can be activated by setting antialias_shader=1 (or 2)

          antialias_shader=0 (default)

        Open Source and Incentive

        • run pml and py script with load
        • support ccp4 maps with mode 0 and 1
        • Simple text editor to edit pymolrc (Tk GUI: File > Edit pymolrc)
        • improved mmCIF file loading (load multi-model entries, read secondary structure)
        • Commands
          • volume now takes a ramp as its third argument
          • volume_color can color volumes by custom ramps and ramp presets
          • volume_ramp_new can register a new volume ramp preset
          • desaturate desaturates colors
          • join_states creates a multi-state object from multiple objects
          • alphatoall transfers atom properties from the CA atoms to the full residue
          • loadall loads all files from a file name pattern
          • centerofmass calculates the center of mass
          • extra_fit performs a many-to-one alignment
          • api queries API details about a command
        • Settings
          • volume_mode to toggle between post-classified and pre-integrated volume rendering
          • intensity adjustment when changing volume_layers
          • antialias_shader

        Bug Fixes

        • fix distorted labels with stereo walleye/crosseye
        • fix cartoon picking doesn't honor masking atoms/objects
        • fix cyclic nucleotide was marked as polymer
        • fix atom properties: assign empty string (Incentive PyMOL only)

        PyMOL v1.7

        Incentive Only

        Open Source and Incentive

        • get_renderer command to return information about the graphics card

        • focal_blur to blur images away from the focal point

        • get_bond for retrieving bond properties

        • fetch from PubChem with SID and CID codes

        • get_version expanded to return detailed build information

        • cmd.load_coords can now take any Python array (sized Nx3) and extend an object

        • New Settings

          • pdb_conect_nodup, don't write bond-order duplicated PDB CONECT records (available in Open-Source PyMOL since SVN rev 4088)

          • session_embeds_data, to encapsulate ancillary information inside a session

          • map_auto_expand_sym, takes symmetry from map if molecular object doesn’t have symmetry information

        • 3f atom-level settings now supported
        • Atom-state level settings

        • Color settings are now stored as colors, they can be set as either colors, hex (i.e, 0xRRGGBB), or float values ( [1., 1., 1.])

        • Suppress writing PDB “segi” field to PDB file if ignore_pdb_segi=1

        • Improved the PDB Loader GUI

        • PyMOL now reads space group from CCP4 maps

        • PyMOL treats empty space group like P1 (for best support of map formats which do not have a space group)

        • New selection keywords sidechainbackbonemetals

        • Improved and extended the Filter Wizard (Wizard > Filter).

        PyMOL v1.6

        Incentive Only 

        • Presets for coloring by representation (Color > C > by rep)
        • Settings
          • Over 500 settings are now documented in the Settings > Edit All GUI
          • The Settings > Edit All GUI was refactored to allow window resizing, mouse wheel scrolling and searching
        • Iterate and alter have improved performance
        • Molecular Morphing is now easier and more complete
          • Just click A > generate > morph for painless morphing
          • Multi-state morphs
        • "ramps" in C (color) menu
        • Arbitrary object-level and atom-level properties
        • Mouse wheel scrolls object-menu-panel and other scrollable widgets
        • Spectrum command enhanced to take the new properties as expression
        • Better tracking of hydrogens when editing with the Builder

        Open Source and Incentive

        • Completed OpenGL engine update; improved graphics performance.
        • High-speed fonts, indicators, and 2D drawables (menus)
        • Support sweep_angle setting with Program > Scene Loop Nutate/Rock
        • Add bz2 support for reading PDB/MAE/MOE/... files
        • Add support for width/height units in png command
        • New command line argument "-y": Exit on error
        • Support object=aln argument with alignto command
        • VMD plugins have been updated
        • New commands: split_chains, mse2met
        • Spectrum command enhanced to take color lists like spectrumany
        • ANISOU records are now saved if present
        • Fixed alignment objects from super do not contain N atoms
        • Fixed writing PDB files
          • END before ENDMDL (SF-3496006)
          • always right justify resn (SF-3539436)
        • Fixed crash when loading with connect_mode=2
        • Fixed shortcut auto-completion with exact prefixes
        • Feedback fixes
        • Fixed leading whitespace parsing in LITERAL parsing mode
        • Fixed reading last ANISOU record from PDB file
        • Surface lighting was improved for more realistic lighting

        Old Surface RenderingNew Surface Rendering

        • Fixed Scripts ending on ""
        • Cealign alignment object: support for multiple alignments

        PyMOL v1.5

        (I) -- Incentive PyMOL only; (I+O) -- Incentive PyMOL and Open-source PyMOL

        Real-time Rendering Performance

        • Increased real-time rendering performance (I+O)

        • Real-world, real-time rendering example of 250,000 atoms:

          • Lines: 28 Hz → 226 Hz (707% increase!)

          • Cartoons: 7 Hz → 47 Hz (571% increase!)

          • Sticks: 2.1 Hz → 37 Hz (1661% increase!)

          • Surfaces: 6.0 Hz → 70 Hz (1,066% increase!)

        Real-time Rendering Improvements

        Comparison of Real-time Rendering Improvements
        (left column: old rendering; right column: new rendering)

        All images shown here are from real-time rendering not ray tracing
        • Support for bg_gradient when ray tracing (I+O)

        • Many more non-standard nucleic acids (PSU, 5MU, 7MG, MIA, H2U, 4SU, MA6, UR3, 5MC, 40C, 2MG, TM2, 2MG) render correctly as cartoons (I+O)

        • Surface color smoothing (I+O)

        • Frame buffer-based antialiasing for real-time rendering (I+O)

        • Optimized anaglyph colors and intensities for an improved 3D viewing experience (I+O)

        Comparison of standard anaglyph (left) to PyMOL's optimized anaglyph (right)
        • Real-time and ray-traced ambient occlusion (I+O)

        Ambient occlusion hinting for surfaces

        Molecular Modeling

        • undo now supports changes in: addition/removal of atoms and fragments, changes in atom type, valence, object creation, and more (I)

        • Improved feedback for the clean command (I)

        Mac OS X

        • Support for Mac OS X 10.7 (Lion) (I)

        • MacPyMOL now comes with a Mac-friendly DMG installer (I)

        • Restored Space Navigator 3D support (I)

        Other Enhancements

        • Molecular weight (A > Compute > Molecular Weight) calculation supporting explicit structure and implicit (PyMOL auto-adds hydrogens) (I+O)

        • Selection generation, A > Generate > Selection > ..., for (I+O)

          • polar hydrogens
          • non-polar hydrogen
          • hydrogen bond donors
          • hydrogen bond acceptors
          • surface atoms
        • Support for reading compressed Maestro (.maegz)** and PyMOL session files (.pze, pzw, .pse.gz, .psw.gz) (I)

        • Added Show > Valence and Hide > Valence for fine-grained valence display control (I+O)

        • Added the get_viewport command (I+O)

        • Surface-based atom selecting/picking via the mouse (I+O)

        • New mouse mode for light positioning (I+O)

        • Many Fixes (I+O)

        (I) -- Incentive PyMOL only

        (I+O) -- Incentive PyMOL and Open-source PyMOL

        PyMOL v1.4

        • New 64-bit MacPyMOL allows Mac users to access more than 4 GB of memory

        • Volume visualization for unique display of volumetric data and simultaneous visualization of multiple iso-surfaces (see

        • Electron density map generation from reflection data (Mac and Linux only, Windows coming soon)

        • Stereochemical labeling

        • Improved Atom Typing; MacroModel and SYBYL/MOL2 support

        • OpenGL Shaders (GLSL) for improved on-screen rendering (cartoons, sticks, surfaces, volumes)

        • Dynamic measurements (distances, bond angles and dihedral angles)

        • File > Save Molecule now allows saving of multiple files, multi-state PDBs to a single file, and multi-state PDBs to multiple files

        • Improved State Handling makes operations on multi-state objects easier

        • Built using updated and Schrödinger-compatible distribution of Python (v2.7)

        • PyMOL Web GUI (PWG)

        • Several bug fixes

        PyMOL v1.4.1

        • MTZ map reading now works on all our supported platforms and architectures.

        • Transparent ribbons – just "set ribbon_transparency, X" like other transparency settings.

        • Improved state handling makes operations on multi-state objects easier.

        • GLSL shaders now support depth cueing/fogging.

        • New background gradient. “set bg_gradient”.

        • Map resolution displayed as Angstroms, not 1/d^2, from MTZ file.

        • Elementary volume ray tracing; “set ray_volume”.

        • Cross-platform bug fixes.

        PyMOL v1.3.r1

        • Fully dynamic measures

        • A > Generate > Selection > Surface Residues

        • Fixed dihedral bug

        • Added filtering step in File>Save Molecule...

        • Added mouse-mode tracking, improved neighbor finding, mixed-mode measurements to the Measurement Wizard

        • new cealign command; cealign is a new command that performs protein structure alignment using the CE algorithm.

        • updated fetch command; this command has the new capability of downloading omit maps from the EDS server.

        • new obscure command to beautifully hide proprietary data

        • many new settings for controlling measurements