id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1379 Failure on OSX 10.11 chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: Darwin-15.6.0-x86_64-i386-64bit ChimeraX Version: 0.7 (2018-08-07) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.7 (2018-08-07) OpenGL version: 4.1 INTEL-10.14.74 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc. How to cite UCSF ChimeraX open ""/Users/leslieleepedraza/Downloads/5yx2 (1).pdb"" Opened PDB data containing 8380 atoms and 8616 bonds Chain information for 5yx2 (1).pdb #1 --- Chain | Description A D | DNA (cytosine-5)-methyltransferase 3A B C | DNA (cytosine-5)-methyltransferase 3-like E F | DNA (25-mer) Error processing trigger ""frame drawn"" Traceback (most recent call last): File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/triggerset.py"", line 126, in invoke return self._func(self._name, data) File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/filehistory.py"", line 69, in t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb()) File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/filehistory.py"", line 81, in capture_thumbnails_cb fs.capture_image(models, ses) File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/filehistory.py"", line 152, in capture_image self.image = models_image(session, models, size) File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/filehistory.py"", line 209, in models_image image = v.image(width, height, camera = c, drawings = models) File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/view.py"", line 397, in image from PIL import Image File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/Image.py"", line 60, in from . import _imaging as core ImportError: dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found: _clock_gettime Referenced from: /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12) Expected in: /usr/lib/libSystem.B.dylib in /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib save image ""/Users/leslieleepedraza/Desktop/CORE Papers L13 onward/5YX2.png"" width 345 height 457 Traceback (most recent call last):   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/gui.py"", line 744, in     save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess))   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/gui.py"", line 532, in file_save_cb     self.save_dialog.display(self, session)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 141, in display     fmt.save(session, filename)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 40, in save     return self._save(session, filename)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 269, in save     run(session, cmd)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/run.py"", line 31, in run     results = command.run(text, log=log)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2561, in run     result = ci.function(session, **kw_args)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/save.py"", line 61, in save     fmt.export(session, filename, fmt.nicknames[0], **kw)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/io.py"", line 198, in export     result = self.export_func(session, path, **kw)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/image.py"", line 97, in save_image     from PIL import PngImagePlugin   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/PngImagePlugin.py"", line 39, in     from . import Image, ImageFile, ImagePalette   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/Image.py"", line 60, in     from . import _imaging as core ImportError: dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found: _clock_gettime   Referenced from: /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12)   Expected in: /usr/lib/libSystem.B.dylib  in /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib ImportError: dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found: _clock_gettime Referenced from: /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12) Expected in: /usr/lib/libSystem.B.dylib in /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/Image.py"", line 60, in from . import _imaging as core See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. save image ""/Users/leslieleepedraza/Desktop/CORE Papers L13 onward/5YX2.png"" width 345 height 457 Traceback (most recent call last):   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/gui.py"", line 744, in     save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess))   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/gui.py"", line 532, in file_save_cb     self.save_dialog.display(self, session)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 141, in display     fmt.save(session, filename)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 40, in save     return self._save(session, filename)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/save_dialog.py"", line 269, in save     run(session, cmd)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/run.py"", line 31, in run     results = command.run(text, log=log)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/cli.py"", line 2561, in run     result = ci.function(session, **kw_args)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/commands/save.py"", line 61, in save     fmt.export(session, filename, fmt.nicknames[0], **kw)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/io.py"", line 198, in export     result = self.export_func(session, path, **kw)   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/image.py"", line 97, in save_image     from PIL import PngImagePlugin   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/PngImagePlugin.py"", line 39, in     from . import Image, ImageFile, ImagePalette   File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/Image.py"", line 60, in     from . import _imaging as core ImportError: dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found: _clock_gettime   Referenced from: /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12)   Expected in: /usr/lib/libSystem.B.dylib  in /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib ImportError: dlopen(/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/_imaging.cpython-36m-darwin.so, 2): Symbol not found: _clock_gettime Referenced from: /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib (which was built for Mac OS X 10.12) Expected in: /usr/lib/libSystem.B.dylib in /Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/.dylibs/liblzma.5.dylib File ""/Volumes/ChimeraXInstaller/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/PIL/Image.py"", line 60, in from . import _imaging as core See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. OpenGL version: 4.1 INTEL-10.14.74 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc. }}} " defect closed normal Platform not a bug all ChimeraX