id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1910 Crash with symmetry expansion James.Conway@… Tom Goddard "{{{ I am using the ""sym"" command in ChimeraX to expand an asymmetric unit to full icosahedral symmetry, MacOSX 10.14.4, ChimeraX latest daily build 0.9 (2019-05-01). The asymmetric unit is large, with 43 copies of the major capsid protein, but I have stripped it down to just 7656 alpha-carbon atoms total. It is read into ChimeraX from a PDB-format file. The sym command is: sym #1 i,2n5r center 559.3,559.3,559.3 I have quit other programs, and the Mac Pro has 64 GBytes of RAM and two AMD FirePro D700 graphics cards (6 GBytes each). The outcome varies from try to try: 1) Succeeds, and I can manipulate the large capsid model fine. 2) The screen returns to the login window, I login and ChimeraX is running with the correct result shown, and I can manipulate the large capsid model fine. 3) My session is logged out - I log in to a new session, have to start again. I haven't figured out what triggers each outcome, but I assume its a memory issue somewhere. A preferred outcome would be for ChimeraX to more gracefully indicate what the problem is, but I also wonder if using the PDB format is part of the problem, although expanding the symmetry like this should result in 459360 atoms, less that the 1,000,000 limit for PDB files. I assumed Chimera would perform poorly with this large model, but any advice appreciated. James Conway ---------------------------------------------------------------------- James Conway, PhD., Professor, Department of Structural Biology Director, Molecular Biophysics and Structural Biology Graduate Program University of Pittsburgh School of Medicine Biomedical Science Tower 3, Room 2047 3501 5th Ave Pittsburgh, PA 15213 U.S.A. Phone: +1-412-383-9847 Fax: +1-412-648-8998 Email: jxc100@pitt.edu Web: http://www.structbio.pitt.edu/index.php/12-faculty/18-james-conway ---------------------------------------------------------------------- }}} " defect closed normal Higher-Order Structure nonchimerax Eric Pettersen all ChimeraX