PyMOL v1.7.0.0 Notes

Release Date: January 14, 2014.

Graphics

  • new labels visual additions : connectors, backgrounds, and outlines
    • Note: We are building an interface that will make it easier to control labels interactively so that you won’t need to remember all of these settings explicitly, but these settings show how we have added flexibility and controls into labels
  • New callouts for scene-based labels.

Commands

  • New: get_renderer to return information about the graphics renderer
  • New: get_bond to get bond properties
  • fetch from pubchem with cid and sid codes
  • Expanded get_version command to return more detailed build information (get_version -1)
  • cmd.load_coords can now take any Python array (sized Nx3) and create an object from it
  • New: callout to create scene-based labels
  • Remove deprecated mray

Settings

  • More settings annotated in Settings > Edit All > ...
  • New: session_embeds_data, to encapsulate ancillary information inside a session
  • 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
  • Many new labels settings
  • cartoon_side_chain_helper is now atom-level

Wizards and Usability

  • New Search Wizard (CTRL-F) to find objects and selections in the Object Menu Panel
  • New selection keywords sidechain, backbone, metals
  • Improved and extended the Filter Wizard (Wizard > Filter).
  • Access settings and properties from the iterate/alter commands via “s.” and “p.”
  • Improved the PDB Loader GUI

Map Symmetry Handling

  • read space group from CCP4 maps
  • handle empty space group like P1 (for best support of map formats which do not have a space group)
  • map_auto_expand_sym: take symmetry from map if molecular object doesn’t have symmetry information

Beta Features

Bug Fixes

  • Dynamic measures now saved to session files
  • ‘isolevel’ now updates with GLSL shaders
  • Fixed F-keys recalling scenes from loaded sessions
  • Tcl/Tk X11 window placement fixed on Mac OS X
  • Tcl/Tk Save multiple to one file fixed
  • Fixed writing multi MOL2 files
  • Fixed pair_fit with one atom pair
  • Fixed sequence viewer background/label colors
  • Stopped cealign from inverting target structure
  • Fixed preserve use_shaders setting when loading session files
  • Fixed atom order after h_add
  • Fixed load_traj with stop/max arguments
  • Fixed bg_rgb settings for old session files
  • Fixed crashes with graphics related bugs
  • Fixed two_sided_lighting bug with cartoon shaders
  • Improved util.chainbow do smarter coloring
  • Gracefully reject writing MOL format with >999 atoms
  • Fix saving MOL2 format with empty atom name
  • Fix ray+png in batch mode ray traces twice
  • apbs_tools PDB writing: disable putting spaces before dashes
  • Fix molecular weight w/ aromatic bonds & missing hydrogens
  • disable seq_view in mpng, this broke movie export

PyMOL v1.7.0.1 Hotfix Notes

  • fix pymolrc reading on Windows
  • fix focal_blur on Windows (update PIL)

PyMOL v1.7.0.3 Hotfix Notes

  • Windows 32bit not working on some older Intel cards
  • Picking problem on some cartoons

PyMOL v1.7.0.5 Hotfix Notes

  • don’t disable all shaders if geometry shaders are not available
  • grid_mode support for volumes
  • many z-depth issues for labels and connectors in immediate, shader, and ray tracing (all renderings should now look almost exactly the same)
  • background in front of text with use_shaders=0
  • label picking broken with use_shaders=0
  • character rendering in ray tracing
  • clipped text in multi-line labels (shader on and off)
  • CGO colors ignored with ALPHA
  • cartoon memory leak
  • hidden groups flash in scene based movies
  • “A > find > polar contact > just intra-side chain” broken
  • “scene auto, update” broken
  • small solvent_radius crashes Surface generation
 
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