Release Date: Apr-20-2016

• iterate exposes atom-level settings (e.g. s.sphere_scale), Incentive feature since PyMOL 1.7

• 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)
• ignore_case_chain setting (ignore_case=1 default restored in 1.8.0.5)
• collada_background_box (off by default, previous versions unconditionally created a large box to mimic the scene background color)

• support atom name/resn/segi with more than 4 letters (e.g. from CIF files)
• MOL2
  • loading
    • improve resn reconstruction from subst_name
    • improve formal_charge guessing
  • export
    • write SUBSTRUCTURE record for chain support
• MAE loading: sort atoms
• amber topology loading: set all bond orders to 1 instead of 0

• new “Distances between rings” measurement mode in Measurements Wizard
• new “byring” selection operator
• new distance mode=4: distance between centroids

• cartoon representation
  • cartoon dash: New loop-like cartoon type which skips every second segment
  • auto-detect CA-only models for cartoon and ribbon (no cartoon_trace_atoms needed)

• enable ignore_case and ignore_case_chain for “rms” and “update”
• grid_mode=3: prid per object-state

• iterate/alter
  • list(s) → list of atom-level setting indices (or atom-state-level settings with iterate_state)
  • improve exception handling and error reporting
  • disable automatic text_type assignment with atom_type_format=““ (empty string)

• APBS Tools: various UI fixes from Pymol-script-repo
• fix missing caps with different stick_radius
• fix label_relative_mode=2 in side-by-side stereo
• fix label_connector_width in side-by-side stereo
• fix cylinder half-bond antialiasing in grid_mode
• fix crash with cache_frames and mset
• mmCIF secondary structure loading: assign “ss” to all atoms, not only CA
• command execution after reinitialize (https://sourceforge.net/p/pymol/mailman/message/34842037/)
• fix picking ribbons w/ ribbon_as_cylinders=on or trilines=on

• fix “A > generate > vacuum electrostatics”
• MacPyMOL: fix “Get View” button

• fix mutagenesis wizard “No Mutation” (update and rms commands)
• new setting “pick32bit” allows forcing of 16bit picking
• fixed pse_binary_dump + pse_export_version<1.77 combination

• fix crash with ray tracing very large images
• fix crash with “align” and atoms without coordinates
• fix automatic stereochemistry labeling

• fix picking bug: wrong picking after re-enabling previously picked objects
• fix restoring “filter” wizard from PyMOL 1.6 session files
• fix “scene auto, clear” (Scene > Delete)

• fix quadbuffer stereo non-black background issue
• MAE import “s_m_ribbon_color_rgb” support