New Features

PyMOL 1.8.4

PyMOL 1.8.2

  • cartoon_gap_cutoff: draw dashed cartoon over gaps of size < cartoon_gap_cutoff
  • auto_show_classified: When loading a file, show cartoon for polymer, sticks for organic, and spheres for inorganic molecules (Setting > Auto Show... > ... by Classification)
  • new “Distances between rings” measurement mode in Measurements Wizard
  • MOL2 file support improvements

      PyMOL 1.8.0

      See also

      Open Source and Incentive

      • changed defaults:
      • 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