PyMOL v1.8.0.0 Notes

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/

New Features

  • (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

Refactoring

  • 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

PyMOL API

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

Settings

  • 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.

Misc

  • 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)

Mobile PyMOL

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

Bug Fixes

  • 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

PyMOL v1.8.0.1 Hotfix Notes (Nov 24, 2015)

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

PyMOL v1.8.0.2 Hotfix Notes (Nov 30, 2015)

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

PyMOL v1.8.0.3 Hotfix Notes (Dec 18, 2015)

  • 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

PyMOL v1.8.0.4 Hotfix Notes (Jan 26, 2016)

  • 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

PyMOL v1.8.0.5 Hotfix Notes (Feb 8, 2016)

PyMOL v1.8.0.6 Hotfix Notes (Mar 3, 2016)

  • 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

PyMOL v1.8.0.7 Hotfix Notes (Apr 6, 2016)

  • 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

PyMOL v1.8.0.8 Hotfix Notes (Jul 21, 2016)

  • 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
 
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