id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4290 Various session save/restore errors sitins07@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.17763 ChimeraX Version: 1.2.dev202011140750 (2020-11-14 07:50:08 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2.dev202011140750 (2020-11-14) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""D:/Useful things/EV6-EV8-EV9_j1661_session.cxs"" Unable to restore session, resetting. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 684, in restore obj = sm.restore_snapshot(self, data) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 565, in restore_snapshot m.add([model], _from_session=True) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 663, in add self.add(children, parent=model, _notify=False, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 663, in add self.add(children, parent=model, _notify=False, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 650, in add p = self._parent_for_added_model(model, parent, root_model = root_model) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 714, in _parent_for_added_model raise ValueError('Tried to add model %s to parent %s with incompatible id' ValueError: Tried to add model j1685_52A_run_class001.mrc #1.1 to parent group #1.1 with incompatible id Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 684, in restore obj = sm.restore_snapshot(self, data) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 565, in restore_snapshot m.add([model], _from_session=True) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 663, in add self.add(children, parent=model, _notify=False, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 663, in add self.add(children, parent=model, _notify=False, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 650, in add p = self._parent_for_added_model(model, parent, root_model = root_model) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 714, in _parent_for_added_model raise ValueError('Tried to add model %s to parent %s with incompatible id' ValueError: Tried to add model j1685_52A_run_class001.mrc #1.1 to parent group #1.1 with incompatible id During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\ui\gui.py"", line 533, in dropEvent _open_dropped_file(self.session, p) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\ui\gui.py"", line 1754, in _open_dropped_file run(session, 'open %s' % FileNameArg.unparse(path)) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2835, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 105, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2835, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 169, in provider_open models, status = collated_open(session, None, [data], data_format, _add_models, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\open_command\cmd.py"", line 412, in collated_open return func(*func_args, **func_kw) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 26, in open return cxs_open(session, data, **kw) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 944, in open session.restore(stream, path=path, resize_window=resize_window) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 692, in restore self.reset() File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 502, in reset sm.reset_state(container, self) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 570, in reset_state self.close([m for m in self.list() if not m.SESSION_ENDURING]) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 888, in close self.remove(mopen) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\models.py"", line 858, in remove m.removed_from_session(session) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\atomic\structure.py"", line 132, in removed_from_session self._graphics_updater.remove_structure(self) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\atomic\structure.py"", line 1548, in remove_structure self._structures.remove(s) KeyError: KeyError: File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\atomic\structure.py"", line 1548, in remove_structure self._structures.remove(s) See log for complete Python traceback. > open D:/Projects/translocation/G1/j1663_run_class001.mrc Opened j1663_run_class001.mrc as #2, grid size 288,288,288, pixel 1.16, shown at level 0.125, step 2, values float32 > open D:/Projects/translocation/G1/j1664_run_class001.mrc Opened j1664_run_class001.mrc as #3, grid size 288,288,288, pixel 1.16, shown at level 0.0998, step 2, values float32 > open D:/Projects/translocation/G1/j1687_run_class001.mrc Opened j1687_run_class001.mrc as #4, grid size 288,288,288, pixel 1.16, shown at level 0.0535, step 2, values float32 > open D:/Projects/translocation/G1/j1685_run_class001.mrc Opened j1685_run_class001.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 0.055, step 2, values float32 > open D:/Projects/translocation/G1/j1686_run_class001.mrc Opened j1686_run_class001.mrc as #6, grid size 288,288,288, pixel 1.16, shown at level 0.0777, step 2, values float32 > close #1 > hide #!2 models > show #!2 models > rename #2-6 id #7 > rename #7 EV6_rotation-d4d5 > hide #!7 models > open D:/Projects/translocation/G1/j1676_run_class001.mrc Opened j1676_run_class001.mrc as #2, grid size 288,288,288, pixel 1.16, shown at level 0.07, step 2, values float32 > open D:/Projects/translocation/G1/j1677_run_class001.mrc Opened j1677_run_class001.mrc as #3, grid size 288,288,288, pixel 1.16, shown at level 0.0562, step 2, values float32 > open D:/Projects/translocation/G1/j1689_run_class001.mrc Opened j1689_run_class001.mrc as #4, grid size 288,288,288, pixel 1.16, shown at level 0.0553, step 2, values float32 > open D:/Projects/translocation/G1/j1693_run_class001.mrc Opened j1693_run_class001.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 0.114, step 2, values float32 > open D:/Projects/translocation/G1/j1688_run_class001.mrc Opened j1688_run_class001.mrc as #6, grid size 288,288,288, pixel 1.16, shown at level 0.0556, step 2, values float32 > rename #2-6 EV8_towards-head id #8 > rename #7 id #2 > rename #8 id #3 > hide #!3 models > open D:/Projects/translocation/G1/j1680_run_class001.mrc Opened j1680_run_class001.mrc as #4, grid size 288,288,288, pixel 1.16, shown at level 0.0544, step 2, values float32 > open D:/Projects/translocation/G1/j1679_run_class001.mrc Opened j1679_run_class001.mrc as #5, grid size 288,288,288, pixel 1.16, shown at level 0.061, step 2, values float32 > open D:/Projects/translocation/G1/j1694_run_class001.mrc Opened j1694_run_class001.mrc as #6, grid size 288,288,288, pixel 1.16, shown at level 0.0522, step 2, values float32 > open D:/Projects/translocation/G1/j1696_run_class001.mrc Opened j1696_run_class001.mrc as #7, grid size 288,288,288, pixel 1.16, shown at level 0.0603, step 2, values float32 > open D:/Projects/translocation/G1/j1695_run_class001.mrc Opened j1695_run_class001.mrc as #8, grid size 288,288,288, pixel 1.16, shown at level 0.0533, step 2, values float32 > rename #4-8 EV9_towards-decoding id #9 > rename #9 id #4 > close #1 > select all 35 models selected > volume sel & #!4.1-5 step 1 > show #!2 models > show #!3 models > show #!1 models > select all 35 models selected > volume sel step 1 An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\view.py"", line 165, in draw self._draw_scene(camera, drawings) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\view.py"", line 247, in _draw_scene draw_highlight_outline(r, highlight_drawings, color = self._highlight_color, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1567, in draw_highlight_outline _draw_multiple(drawings, r, Drawing.HIGHLIGHT_DRAW_PASS) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1511, in _draw_multiple d.draw(renderer, draw_pass) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 751, in draw self.draw_self(renderer, draw_pass) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 765, in draw_self self._draw_geometry(renderer, highlighted_only = True) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 785, in _draw_geometry ds.activate_bindings(renderer) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1858, in activate_bindings self.update_buffers() File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\drawing.py"", line 1846, in update_buffers b.update_buffer_data(data) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\graphics\opengl.py"", line 2606, in update_buffer_data GL.glBufferData(btype, size, d, GL.GL_STATIC_DRAW) File ""src/latebind.pyx"", line 51, in OpenGL_accelerate.latebind.Curry.__call__ File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\OpenGL\GL\VERSION\GL_1_5.py"", line 89, in glBufferData return baseOperation( target, size, data, usage ) File ""src/latebind.pyx"", line 39, in OpenGL_accelerate.latebind.LateBind.__call__ File ""src/wrapper.pyx"", line 318, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/wrapper.pyx"", line 311, in OpenGL_accelerate.wrapper.Wrapper.__call__ File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1285, description = b'out of memory', baseOperation = glBufferData, pyArgs = ( GL_ELEMENT_ARRAY_BUFFER, 10076496, array([[ 0, 3, 1], [ 2, 3, 0], [ 5, 3, 7], ..., ..., GL_STATIC_DRAW, ), cArgs = ( GL_ELEMENT_ARRAY_BUFFER, 10076496, array([[ 0, 3, 1], [ 2, 3, 0], [ 5, 3, 7], ..., ..., GL_STATIC_DRAW, ), cArguments = ( GL_ELEMENT_ARRAY_BUFFER, 10076496, array([[ 0, 3, 1], [ 2, 3, 0], [ 5, 3, 7], ..., ..., GL_STATIC_DRAW, ) ) > volume sel level 0.025 > hide #!2 models > show #!2 models > save D:/Projects/translocation/G3/Figures/g3.cxs includeMaps true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\map\session.py"", line 311, in state_from_grid_data s['array'] = b64encode(compress(dt.matrix().tobytes())) MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 583, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> : Error while saving session data for 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> ValueError: error processing: 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> : Error while saving session data for 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\map\session.py"", line 311, in state_from_grid_data s['array'] = b64encode(compress(dt.matrix().tobytes())) MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\ui\gui.py"", line 1574, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 102, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 113, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 48, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2835, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2835, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 78, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 583, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> : Error while saving session data for 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> ValueError: error processing: 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> : Error while saving session data for 'models' -> -> 'surface' -> 'j1695_run_class001.mrc' -> File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2.1 models > show #!2.1 models > save D:/Projects/translocation/G3/Figures/g3.cxs includeMaps true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\map\session.py"", line 311, in state_from_grid_data s['array'] = b64encode(compress(dt.matrix().tobytes())) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\gzip.py"", line 540, in compress f.write(data) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\gzip.py"", line 280, in write self.fileobj.write(self.compress.compress(data)) MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 583, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> : Error while saving session data for 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> ValueError: error processing: 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> : Error while saving session data for 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 280, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\map\session.py"", line 311, in state_from_grid_data s['array'] = b64encode(compress(dt.matrix().tobytes())) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\gzip.py"", line 540, in compress f.write(data) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\gzip.py"", line 280, in write self.fileobj.write(self.compress.compress(data)) MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 259, in discovery self.processed[key] = self.process(obj, parents) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 283, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\ui\gui.py"", line 1574, in action.triggered.connect(lambda arg, cb = callback: cb()) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 102, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 113, in show_save_file_dialog _dlg.display(session, **kw) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 48, in display run(session, cmd) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\commands\run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2835, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 66, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2835, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\save_command\cmd.py"", line 78, in provider_save provider_info.bundle_info.run_provider(session, provider_info.format_name, File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 79, in save return cxs_save(session, path, **kw) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 839, in save session.save(output, version=version, include_maps=include_maps) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 583, in save mgr.discovery(self._state_containers) File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> : Error while saving session data for 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> ValueError: error processing: 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> : Error while saving session data for 'models' -> -> 'surface' -> 'j1676_run_class001.mrc' -> File ""C:\Program Files\ChimeraX 1.2.dev202011140750\bin\lib\site- packages\chimerax\core\session.py"", line 261, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 431.94 OpenGL renderer: Quadro P4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision 5820 Tower OS: Microsoft Windows 10 Enterprise (Build 17763) Memory: 33,716,879,360 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Xeon(R) W-2135 CPU @ 3.70GHz OSLanguage: en-US Locale: ('en_US', 'cp1252') PyQt version: 5.15.1 Compiled Qt version: 5.15.1 Runtime Qt version: 5.15.1 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.11.8 cftime: 1.2.1 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.9.3 ChimeraX-AtomicLibrary: 1.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.dev202011140750 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.1 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.3.1 ChimeraX-PDB: 2.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.2.2 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.3.1 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.6.3 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.5.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 netifaces: 0.10.9 networkx: 2.5 numexpr: 2.7.1 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.4 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 20.2.3 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.8 psutil: 5.7.2 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.1 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.1 python-dateutil: 2.8.1 pytz: 2020.4 pywin32: 228 pyzmq: 20.0.0 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.0 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.35.1 WMI: 1.5.1 }}} " defect closed normal Sessions duplicate Greg Couch all ChimeraX