Hi Pete, Short Solution:
Please save complete symmetry information for your maps before saving with PyMOL v1.5.0.1. Copying the symmetry information from a PDB to the map fixes this problem because it updates the map's space group field. So, typing symmetry_copy src_pdb_file, target_map before saving the file allows me to re-open that session file in PyMOL v1.5.0 and later. Note, you can copy symmetry information from one object to another using, "symmetry_copy src_object, target_object". You can also set the symmetry information by hand, using, the "set_symmetry" command. In some cases I realize this won't help, so we'll put out a new build ASAP. Detailed Answer: The problem occurs when PyMOL tries to load a session with a map that doesn't have complete symmetry information. In the past PyMOL considered symmetry information for PDBs to be the crystal information plus the space group, whereas it considered symmetry information for maps to be only crystal information. This is why you couldn't replicate a map outside the unit cell. In PyMOL v1.5 we "fixed" that, making PDBs and maps share the same underlying idea of what symmetry information is. This allows you to use symmetry_copy to shuttle the complete information to/from PDBs _and_ maps. If you have any legacy data that can be shared, please let us know and we'll keep it around for testing future builds. Cheers, -- Jason On Wed, Feb 15, 2012 at 3:59 PM, Pete Meyer <pame...@mcw.edu> wrote: > Hi Jason, > > This is with the 1.5.0.1 release (source build from pymol-v1.5.0.1.tar.bz2, > md5 8d44de94cff8bce79ce521a1116b0760). > > Sorry if this was a duplicate bug report; I guess I hadn't checked the list > archives well enough. > > Pete > > > Jason Vertrees wrote: >> >> Hi Pete, >> >> You're right -- in v1.5.0 there was this problem which forced us to >> release a "hotfix". PyMOL v1.5.0.1, the current release, fixes this >> problem. >> >> Cheers, >> >> -- Jason >> >> On Wed, Feb 15, 2012 at 2:13 PM, Pete Meyer <pame...@mcw.edu> wrote: >>> >>> Anyone thinking about upgrading to 1.5 should be aware that there's a >>> bug in loading session (pse) files containing map objects. Loading pse >>> files (I checked ones created with 1.2 or 1.4) deletes these objects and >>> reports an error: "ExectiveSetSession-Error: after >>> names.\nExectiveSetSession-Warning: restore may be incomplete." The >>> isomesh/isosurface objects created from the maps aren't deleted, but >>> they're empty (aka not displaying when enabled). >>> >>> Reconstructing the same session from a script didn't show any problems. >>> >>> Pete >>> >>> >>> ------------------------------------------------------------------------------ >>> Virtualization & Cloud Management Using Capacity Planning >>> Cloud computing makes use of virtualization - but cloud computing >>> also focuses on allowing computing to be delivered as a service. >>> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >>> _______________________________________________ >>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> >> >> >> > -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
