PyMOL v1.7.6.0 Notes

Release Date: May-6-2015

PyMOL 1.7.6 is mostly a code refactored release. Most users will have no disadvantage if they don’t upgrade and stay with 1.7.4

This release makes several changes to the PSE (PyMOL Session File) format, so 1.7.4 will not load PSEs from 1.7.6 (see also the new pse_export_version setting).

New Features

  • Order independent transparency for real-time rendering (transparency_mode=3)
  • Warn user if setting a setting on the wrong level
  • mmCIF
    • support CHEM_COMP_BOND from mmCIF file (for updated PDBe mmCIF)
    • support _atom_sites.fract_transf (SCALEn equivalent)
  • Residue information for MOL2 export
  • Find > polar contacts > between chains
  • Don’t disable shaders for all Intel chips (possible because of shader fixes and matured Intel drivers)
  • ChromaDepth: Rainbow coloring by depth (setting: chromadepth)
  • Experimental Retina resolution support in MacPyMOL, enable with –retina command line flag or “Display > Retina Resolution” (1.7.5.4)

Refactoring

  • Complete port of scenes from Python to C++. This improves scene store/recall performance and makes the scene feature available to JyMOL and Mobile PyMOL (no UI yet).
  • adaptive cartoon quality and sampling, depending on number of atoms
  • Reduced memory footprint and session file size of atom data
  • Major reorganisation of shader management
    • eliminates redundant shader reloading
    • perfectly match ray tracing with all lighting settings (ambient, reflect, direct, light_count, etc.)

PyMOL API

  • cmd.extendaa: shortcut for cmd.extend with argument auto-completion
  • expose “reps” to iterate/alter
  • expose “protons” to iterate/alter
  • map_new buffer == -1 → use gaussian_resolution setting

Settings

  • Changed default (!): pdb_conect_nodup=1
  • New: precomputed_lighting, can improve shader rendering performance on slow graphics cards
  • New: pse_export_version, switches to a legacy format when saving PSEs, so far possible (known limitations: volumes, ramps, scenes, CGOs). Values 0 (off) or 1.76 (current) will save the latest format.
  • transparency_mode=3 for order independent multi-layer transparency
  • Removed unused or obsolete settings:
    • use_display_lists
    • simplify_display_lists
    • excl_display_lists_shaders
    • cylinder_shader_ff_workaround
    • cylinders_shader_filter_faces
    • gl_ambient

Bug Fixes

  • fix auto-complete for filenames with spaces
  • make SelectorGetTmp strictly molecular, fixes for example “dss” with group names
  • fix all_states picking
  • fix: grid mode scales down label size incorrectly
  • fix side_chain_helper for hetatm polymer atoms
  • fix .mmd export
  • fix memory leak with connect_mode=4
  • fix loading paths with umlauts from the Tcl/Tk “File” menu
  • fix memory leaks with properties, chempy model loading, set_symmetry, spheroid, copy, cealign
  • fix crash when saving PSE after deleting ramp objects
  • fix ramp coloring with transformed maps (typically affects .cube files)

Known Issues

  • OS X with ATI Radeon R9 graphics cards: spheres and sticks shaders don’t work correctly. There seems to be a bug in the graphics driver. Possible workarounds:
    1. Change these three settings: set render_as_cylinders, 0; set sphere_mode, 0; set nb_spheres_use_shader, 2
    2. We recommend to use PyMOL 1.7.4.4 if you have such a setup.

PyMOL v1.7.6.1 Hotfix Notes (May 26, 2015)

  • fix “File > Open” from drive root on Windows
  • warn if using “unset” on a global setting with default != 0
  • make restoring scenes from PSE tolerant to future versions
  • slice CGO/shader fix

PyMOL v1.7.6.2 Hotfix Notes (May 31, 2015)

  • fix appearance delay for “Display > Sequence”
  • migrate seq_view_label_color=white → front from old PSE
  • fix picking bug with measurement labels
  • fix web/pymolhttpd.py by removing get_scene_dict reference

PyMOL v1.7.6.3 Hotfix Notes (Jul 6, 2015)

  • fix a glDeleteBuffers threading issue (currently Linux and OSX only)
  • fix iterate/alter ref count leak
  • fix “File > Run” in Tcl/Tk GUI (1.7.6.1 regression)
  • avoid non-printable characters in segi after symexp

PyMOL v1.7.6.4 Hotfix Notes (Aug 19, 2015)

  • fix crash after headless (-c) ray tracing empty cartoon
  • fix isosurface (ObjectSurface) all_states rendering
  • fix distance and alignment object partial PSE loading
  • disable impostors on blacklisted OSX ATI Radeon R9
  • fix detection of Boron (vdw and protons properties)

PyMOL v1.7.6.5 Hotfix Notes (Sep 23, 2015)

  • assign protons for B, V, Y elements
  • fix code signing of MacPyMOL
  • fix AxPyMOL crash with multiple displays

PyMOL v1.7.6.6 Hotfix Notes (Oct 2, 2015)

  • fix scene next/previous for Windows 10
  • fix OS X “alternative X11-only” build for OS X 10.11 (El Capitan)
  • fix “File > Run” with spaces in file path

PyMOL v1.7.6.7 Hotfix Notes (Nov 30, 2015)

  • fix MacPyMOL OS X 10.11 crash when double clicking on PDB file in finder
  • fix crash with object selection length >= 1024
  • fix crash with alignment object w/o CGO
  • fix restoring legacy scenes with spaces
  • fix global_transparency_sort issue with surfaces
  • fix PSE loading with atom-state unique ids
 
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