www.pymol.org

PyMOL 2.5

• Multiple-level undo for PyMOL actions
• Curved cartoon cylindrical helices
• Customizable keyboard shortcut menu
• Improved isosurface generation
• Nucleotides from the PDB can now be extended in builder
• Improved Maestro file import
• ... See https://pymol.org/d/media:new25

PyMOL 2.4

• Support for Looking Glass Holographic Displays
• Pi-Pi and Pi-Cation interactions (A > find > pi-interactions)
• WaterMap result presets (A > preset > WaterMap ...)
• APBS Plugin improvements (multi-state assemblies, propka pH calculation)
• Distinguish .mrc and .ccp4 formats (origin interpretation)
• Trajectory handling improvements
• Improved error handling in Python API with exceptions
• ... See https://pymol.org/d/media:new24

PyMOL 2.3

• Atom-level cartoon transparency
• Fast MMTF export
• Sequence viewer gaps display
• ... See https://pymol.org/d/media:new23

PyMOL 2.2

• MAE (Maestro) format export with styling, properties, and group hierarchy
• Nucleic acid mutagenesis wizard
• Stereochemistry labeling with RDKit or $SCHRODINGER backend
• ... See https://pymol.org/d/media:new22

PyMOL 2.1

• new selection keywords "polymer.protein" and "polymer.nucleic"
• SpaceNavigator support on all platforms
• "auto_copy_images" support on all platforms
• ... See https://pymol.org/d/media:new21

PyMOL 2.0

• Unified modern user interface
• Anaconda Python distribution
• Open access incentive executables
• ... See https://pymol.org/d/media:new2

PyMOL 1.8.6

• Fast MMTF load support
• chromadepth ray tracing support (Incentive-only)
• smooth surface edges (Incentive-only)
• ... See https://pymol.org/d/media:new186

PyMOL 1.8.4

• ... See https://pymol.org/d/media:new184

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
• ... See also https://pymol.org/d/media:new182

PyMOL 1.8.0

See also https://pymol.org/d/media:new18

Open Source and Incentive

• changed defaults:
  • 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=0

  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)

  antialias_shader=2

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

• new additions to labels

  • multi-line labels
  • background colors
  • connectors and outlines

• callouts for general labeling

• More settings added to Settings > Edit All GUI

• Many new labels settings

• New Search Wizard (CTRL-F) to find objects and selections in the Object Menu Panel

• Select atoms by coordinates or user-defined properties

• Access settings and properties from the iterate/alter commands via “s.” and “p.”

• AxPyMOL v1.7 Released (for licensed users)

• JyMOL v1.7 Released (for licensed users)

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 sidechain, backbone, metals

• 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

• Fixed Scripts ending on "pymol.py"
• 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 https://pymol.org/volume)

• 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