New Features

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=0
    volume_mode=1
    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
    antialias_shader=0 (default)
    antialias_shader=2
    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

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 "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 http://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