New Features

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