Release Date: Nov-18-2015

Important: The default of the ignore_case setting was changed to on in 1.8.0.0, and restored to off in 1.8.0.5. The problem will be addressed with a new ignore_case_chain setting in 1.8.2. See also https://sourceforge.net/p/pymol/mailman/message/34815599/

• (mm)CIF:
  • add support for discrete=1 loading of CIF files
  • improve multi-model loading (inhomogenious models, pdb_honor_model_number support)
  • support loading multiple objects (“data_” blocks) from one CIF file (multiplex != 0)
  • support _symmetry_equiv.pos_as_xyz, _space_group_symop.operation_xyz
  • set cartoon_trace_atoms and ribbon_trace_atoms for CA-only models
  • load biological unit if assembly setting is set
  • Ignore “auth” identifiers with cif_use_auth=off (default: on)
  • Reimplement reading full sequence from mmCIF (fill in missing CA atoms for polypeptides). Only with cif_use_auth=off. Uses _entity_poly_seq.
  • Improve connect_mode=4 support and performance: Bonding for most common residue types provided in $PYMOL_DATA/chem_comp_bond-top100.cif. Other types are downloaded on the fly from PDBeChem.
  • read metalc and disulf bonds
• New file formats:
  • PDBQT
  • Basic support for PDBML (.xml and .xml.gz extensions)
  • Basic support for CML
• fetch: type=cc downloads from PDBeChem (3-letter codes)
• Render zero-order bonds as dashed lines
• Calculate residue exposure (relative solvent accessible surface area per residue) with get_sasa_relative or from the menu: A > compute > surface area > per residue
• protein-protein interface preset: A > preset > protein interface

• Eliminate more redundancy in PSE files (use pse_export_version for compatibility with older PyMOL versions)
• MAE: reimplemented in C++, improves loading times for .mae files
• Improve picking performance
• mutagenesis wizard: improve “apply” performance

• cmd.set_key() decorator support (@cmd.set_key)
• cmd.get_object_ttt()

• changed default: ignore_case=off. This has major implications for all scripts which are agnostic about identifier case in selection expressions. E.g. “select foo, chain a” won't work for chain A.
• new setting: assembly. Load assembly instead of ASU from mmCIF file
• new setting: cif_use_auth. Controls whether mmCIF “auth” identifiers are used or not (on by
• new setting: cif_keepinmemory. Experimental, use with pymol.querying.cif_get_array
• new setting: pse_binary_dump. Experimental, memory efficient and fast PyMOL session file (PSE) export.
• changed default: scene_buttons=on
• normalize_ccp4_maps=2 → use mean and stdev from file header
• changed default: scene_buttons=on. Show scene buttons by default
• changed default: alignment_as_cylinders=off.

• Symmetry/Cell loading: accept alpha=beta=gamma=0.0, assume orthogonal cell (alpha=beta=gamma=90.0)
• Set protons for unknown atoms to -1 instead of 0 (0 is interpreted as lonepair)
• Properties:
  • alter: derive property type from python type
  • alter: list(p) → list of property names
• real-time ray_transparency_oblique with shaders
• keep IDs when creating new object from selection (restore pre-1.4 behavior)
• updated bundled Schrödinger library for atom typing and stereochemistry (text_type and stereo labeling)
• Tcl/Tk Menus:
  • Radiobuttons for all setting switches
  • Feedback to console when changing a setting
  • Simple font size dialog (Setting > GUI Font Size)

• Chromadepth: The Stereo 3D button is now a 3-state toggle button (Off / Anaglyph / Chromadepth)

• fixes: stick and sphere rendering issues on OS X with ATI Radeon R9 graphics cards (See 1.7.6 known issues)
• fix split_states with non-unique state titles
• support cartoon_trace_atoms for beta-sheets
• alignment object ray tracing
• alignment with atoms w/o coords in a state
• rotate/translate commands with static_singletons and state > 1
• MacPyMOL freezes after being minimized

• fix PSE loading with atom-state unique ids
• fix crash with distances < 1.0 Angstrom

• fix crash with empty alignment object from PSE
• fix 'xyz' export
• fix crash with geometry shaders on Windows (v1.8.0.2-r1)

• fix updating light_count when loading PSE
• fix fetching type=cif with fetch_path not writable
• fix “File > Run… > Cancel” error
• fix loading CGOs from Python without normals and enabling cgo_lighting

• fix “grid_mode” with “internal_gui=0”
• fix picking on double bonds line representation
• fix mol2 format partial charges export
• fix crash with empty CGOs
• fix crash with loading version 1.5 session files
• add toggles to “Settings” menu: cif_use_auth, assembly, connect_mode, normalize_ccp4_maps, normalize_o_maps

• restore “ignore_case=1” default. See also https://sourceforge.net/p/pymol/mailman/message/34815599/
• fix PSE saving of sculpting clash indicators (“bumps”)

• fix selection macros with wildcards and colon (:) residue ranges (1.8.0 regression)
• fix MacPyMOL PSW (PyMOL Show File) fullscreen
• fix line_radius setting affects regular lines

• pse_export_version 1.76 by default (unless pse_binary_dump=1)
• Windows: add missing dlls for numpy and ssl (https) support
• improve performance of * selection keyword
• set_name w/ map: update dependents (mesh, surface, volume)
• fix deleting of user defined properties
• fix load_traj crash w/ state-level settings
• fix crash with pse_binary_dump and ANISOU
• fix COLLADA export crash with transparency
• fix saving PSE w/ mesh w/ deleted map

• fix picking bug: wrong picking after re-enabling previously picked objects
• fix crash when loading non-Amber .top file
• fix pse_binary_dump + pse_export_version=1.766