PyMOL v1.7.4.0 Notes

Release Date: December 3, 2014.

File loading and saving

  • mmCIF
    • fast loading
    • multi-letter chain support
    • loads auth_asym_id as chain and label_asym_id as segi
    • fetch with “fetch 1a00, type=cif”
    • saving (.cif extension, atoms and symmetry only)
    • experimental connect_mode=4 uses components.cif for bonding (file must exist in current directory or COMPONENTS_CIF environment variable)
  • pdb loading: ignore SCALEn in suspicious cases
  • load Desmond idx files
  • load spi (spider) maps
  • load map and mrc extensions as ccp4
  • Python callback objects now stored in PSE files

Graphics

  • improve cartoon and CGO transparency by triangle sorting
  • color CGOs by ramp

Misc

  • gray out missing atoms/residues in seq viewer. Missing residues are read from mmCIF _pdbx_unobs_or_zero_occ_residues records
  • Right-Mouse-Button zoom doesn’t depend on clipping planes anymore
  • added --help and --version command line arguments

MacPyMOL

  • fixed full screen for OS X 10.7+
  • fixed broken Quicktime export
  • MacPyMOL now available with and without bundled Python. The MacPyMOL-v1.7.4.x-syspython.dmg installer uses the system Python (/usr/bin/python2.7) and allows for better integration with scripts that require additional Python modules. We also provide pymol-v1.7.4.x-Darwin-x86_64.tar.gz which uses system Python and the X11 (XQuartz) OpenGL layer.

Settings

  • deprecated full_screen setting in favour of the full_screen command and to handle external full screen control by the window manager

Maestro Integration

  • Import Phase pharmacophores with Maestro’s “View in PyMOL” feature

Python API

  • cmd.set_state_order (new)
  • cmd.load_coords (changed, works on selections now)
  • cmd.load_coordset (was: load_coords)
  • cmd.get_coords (new)
  • cmd.get_coordset (new)
  • cmd.get_volume_field now returns numpy array

Bug Fixes

  • fetch: load PDB from memory if fetch_path not writable
  • line_width < 1

Known Issues

  • Shipped libraries
    • OS X 10.9+, MacPyMOL with bundled Python: scipy.linalg broken. Workaround: Use MacPyMOL-v1.7.4.x-syspython.dmg or pymol-v1.7.4.x-Darwin-x86_64.tar.gz, those use the system Python.
    • OS X 10.7: APBS binary broken. Workaround: Install apbs from fink (or macports, etc.), and in the “PyMOL APBS Tools” panel, point the “APBS binary location” for example to /sw/bin/apbs

PyMOL v1.7.4.1 Hotfix Notes (December 19, 2014)

  • Fixed transparent cartoon cylinders
  • Fixed multi-object CIF export
  • Enable CIF loading in JyMOL
  • pickle protocol 1 for session_compression

PyMOL v1.7.4.2 Hotfix Notes (February 12, 2015)

  • Fixed stereo background color bug
  • Fixed logging settings from the Tcl/Tk menus
  • Fixed picking when cartoon_debug is set

PyMOL v1.7.4.3 Hotfix Notes (February 26, 2015)

  • Fixed walleye and crosseye stereo (regression of v1.7.4.2)

PyMOL v1.7.4.4 Hotfix Notes (March 18, 2015)

  • fix cartoon_ring_mode ring center color
  • fix “Zalman” stereo
  • fix “custom” selection operator
  • fix crash with “copy” command on transformed objects
 
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