PyMOL v1.8.4 Release Notes

Release Date: Oct 10, 2016

Incentive PyMOL only

  • new export file format: MAE (Maestro Structure File)
  • SDF export with properties
  • HETATM classification for MAE import
  • Atom right click > edit label
  • Atom right click > inspect properties: Lists all properties and settings for an atom (wizard atomprops)
  • MacPyMOL space navigator: only receive events if MacPyMOL has focus
  • display_scale_factor: Internal GUI scaling for 4K and Retina displays
  • PDB header gets stored as pdb_header object property if load_object_props_default=*
  • morphing with ligand: minor improvements (fixing of nonbonded during refinement, better ligand detection with method=align)

Incentive/Open-Source PyMOL

  • experimental MMTF load support
  • map export in CCP4 format
  • SDF V3000 import/export support
  • PLY geometry import (as CGO)
  • new command: unset_deep clears all settings on an object
  • new setting: cartoon_all_alt shows cartoon for all alternative conformations
  • setting stick_h_scale: new default 1.0 and not depending on negative stick_radius anymore
  • bymol selection operator: ignore zero-order bonds
  • color menu: isomesh/isosurface negative color
  • improve alignment of residues with unknown resn (e.g. ligands): give a match score of 5 to perfect matches of unknown residue codes. Previously, those got match score -1.
  • use “label_digits” setting with “label” command (e.g. label all, b)
  • do not resize window when loading a session file
  • fix ignored SCALE w/ identity rotation (e.g. 1WAP)
  • new setting: pick_shading: do flat shading for programmable image color analysis
  • experimental cmd.raw_image_callback: post cmd.draw() callback
  • refactored: faster export of cif/sdf/mol2
  • Removed obsolete and broken PMO file support
  • pse_export_version scenes support for versions before 1.7.6

Updates

PyMOL v1.8.4.0-r2 Hotfix Notes (Oct 12, 2016)

  • Windows msi installer: added missing VC100 redistributable for APBS binary
  • added missing umsgpack.py module for MMTF import

PyMOL v1.8.4.1 Hotfix Notes (Oct 21, 2016)

  • fix two-colored ribbon segments (1.8.2 regression)
  • prevent “import cmd”, only allow “from pymol import cmd”
  • MacPyMOL with bundled Python: fix numpy linking

PyMOL v1.8.4.2 Hotfix Notes (Jan 5, 2016)

  • fix line shader for MacOS Sierra
  • new download URL for fetching maps from EDS
  • new download URL for chemical component files
  • fix parsing of MAE files with sub-blocks in tables
 
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