id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3618 vseries problems mmaldo@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-18.7.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-23) Description Hi, I've been getting a number of errors regarding the vseries command, mostly to do wit IndexError: list index out of range. I have a series of 20 volumes. I'm not sure if this is a bug or if I'm not understanding the command properly. When I type ""vseries play #1"" I get no volume series specified, even though my volume series is #1 (#1.1-#1.20). Thank you. Log: UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/mmaldo/Desktop/chimerax/200805 Session 39 3DVA-Rieske.cxs"" > format session Summary of feedback from opening /Users/mmaldo/Desktop/chimerax/200805 Session 39 3DVA-Rieske.cxs --- warnings | restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None notes | Error opening map ""/Users/mmaldo/Desktop/chimerax/200805 Session 39 3DVA-Rieske.cxs"": File 200805 Session 39 3DVA-Rieske.cxs, format mrc MRC header value nsymbt (-1334377196) is invalid opened ChimeraX session Traceback (most recent call last): File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. > open > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_019.mrc Opened FeS_frame_019.mrc, grid size 256,256,256, pixel 1.67, shown at level 0.963, step 1, values float32 Traceback (most recent call last): File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 158, in lambda *args, ft=self._fill_tree: ft(always_rebuild=True)) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] IndexError: list index out of range Error processing trigger ""new frame"": IndexError: list index out of range File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/model_panel/tool.py"", line 203, in _fill_tree parent = item_stack[0] if len(item_stack) == 1 else item_stack[len_id-1] See log for complete Python traceback. > close session > open > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_000.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_019.mrc Opened FeS_frame_000.mrc, grid size 256,256,256, pixel 1.67, shown at level 0.985, step 1, values float32 > open > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/Vr_CIII2_fit_FeS_Ec1_QQ_nolipids-v2.pdb Chain information for Vr_CIII2_fit_FeS_Ec1_QQ_nolipids-v2.pdb #2 --- Chain | Description A M | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G S | No description available H | No description available J V | No description available K | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available T | No description available W | No description available > open > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/Vr_CIII2_fit_Qc1_EQ_nolipids-v2.pdb Chain information for Vr_CIII2_fit_Qc1_EQ_nolipids-v2.pdb #3 --- Chain | Description A M | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G S | No description available H | No description available J V | No description available K | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available T | No description available W | No description available > volume #1.1 level 1.106 > volume #1.1 level 2.227 > volume #1.1 level 2.1 > volume #1.2 level 2.1 > hide atoms > show cartoons > color sequential #1-2/A-K chains palette paired-10 > color sequential #2-3/A-K chains palette paired-10 > color sequential #2-3/M-W chains palette paired-10 > hide #!1 models > show :hem :hec :hea :fes :zn :mg atoms > color byhetero Expected a keyword > select :hem :hec :hea :fes :zn :mg 536 atoms, 568 bonds, 48 pseudobonds, 4 models selected > color sel byhetero > select clear > hide #!2 models > show #!2 models > hide #!3 models > view > morph #2,3 Computed 21 frame morph #4 > coordset #4 1,21 > morph #2,3 Computed 21 frame morph #5 > coordset #5 1,21 > movie record > movie encode /Users/mmaldo/Desktop/movie.mp4 framerate 25.0 Movie saved to /Users/mmaldo/Desktop/movie.mp4 > hide cartoons > ui mousemode rightMode select > hide sel atoms > hide sel atoms > show #1-2/C,D,Q cartoons > close #4 > close #5 > show #!2 models > show #!3 models > hide sel atoms > select up 74 atoms, 64 bonds, 4 pseudobonds, 4 models selected > select up 266 atoms, 284 bonds, 4 pseudobonds, 4 models selected > hide sel atoms > morph #2,3 Computed 21 frame morph #4 > coordset #4 1,21 > save session ""/Users/mmaldo/Desktop/chimerax/200806 Session 41 Rieske > morphs.cxs"" > show #!1 models > hide #!1 models > show #!1 models > volume #1.1 level 2 > volume #1.2 level 2 > volume #1.1 level 1.8 > turn y 180 > turn y 180 > turn y 90 > turn y 90 > turn y 90 > turn y 90 > volume #1.1 level 2 > volume #1.1 level 1.8 > volume #1.2 level 1.8 > turn y 10 > turn y -20 > turn y 15 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > cofr #2/Q > cofr #2/Q > show #!1 models > view > view name front-full-CIII2 > select #1.1 2 models selected > select clear > ui mousemode rightMode translate > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > view name Rieske-zoom > view front-full-CIII2 > view Rieske-zoom > hide #!1 models > open > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_001.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_002.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_003.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_004.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_005.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_006.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_007.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_008.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_009.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_010.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_011.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_012.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_013.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_014.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_015.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_016.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_017.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_018.mrc Opened FeS_frame_001.mrc, grid size 256,256,256, pixel 1.67, shown at level 0.983, step 1, values float32 > close #5 > close #1 > open > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_000.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_001.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_002.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_003.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_004.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_005.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_006.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_007.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_008.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_009.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_010.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_011.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_012.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_013.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_014.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_015.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_016.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_017.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_018.mrc > /Users/mmaldo/Desktop/CIII/VrCIII2_3DVA/J176_3DVA_CIII2alone_FeSmask_5A/cryosparc_P8_J176_component_000/FeS_frame_019.mrc Opened FeS_frame_000.mrc, grid size 256,256,256, pixel 1.67, shown at level 0.985, step 1, values float32 > volume #1.1 level 1.8 > volume #1.2 level 1.8 > volume #1.5 level 1.8 > volume #1.4 level 1.8 > volume #1.3 level 1.8 > volume #1.6 level 1.8 > volume #1.7 level 1.8 > volume #1.8 level 1.8 > volume #1.10 level 1.8 > volume #1.11 level 1.8 > volume #1.12 level 1.8 > volume #1.13 level 1.8 > volume #1.15 level 1.8 > volume #1.16 level 1.8 > volume #1.14 level 1.8 > volume #1.17 level 1.8 > volume #1.18 level 1.8 > volume #1.19 level 1.8 > volume #1.20 level 1.8 > volume #1.20 level 2.923 > volume #1.20 level 1.8 > hide #!1 models > show #!1 models > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > show #!1.3 models > hide #!1.4 models > hide #!1.3 models > hide #!1.5 models > hide #!1.6 models > hide #!1.7 models > hide #!1.8 models > hide #!1.9 models > hide #!1.10 models > hide #!1.11 models > hide #!1.12 models > hide #!1.13 models > hide #!1.14 models > hide #!1.15 models > hide #!1.16 models > hide #!1.17 models > hide #!1.18 models > hide #!1.19 models > hide #!1.20 models > show #!1.20 models > hide #!1.20 models > hide #!1 models > show #!1.1 models > hide #!1.1 models > show #!1.2 models > hide #!1.2 models > show #!1.3 models > hide #!1.3 models > show #!1.1 models > show #!1.20 models > hide #!1.1 models > hide #!4 models > vseries play #1 No volume series specified > vseries play #1.1-1.20 No volume series specified > vseries play #1 loop true No volume series specified > vseries play #1 No volume series specified > vseries play #1.1 No volume series specified > vseries play #1.1,1.20 No volume series specified > vseries play #1.1 No volume series specified > vseries play #1.1-1.20 No volume series specified > vseries play #1.1-1.20 No volume series specified Missing or invalid ""series"" argument: invalid map series specifier > vseries save #1 Rieske threshold 1.8 Traceback (most recent call last): File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 258, in execute cmd.run(cmd_text) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/series/vseries_command.py"", line 189, in vseries_save s = series[0] IndexError: list index out of range IndexError: list index out of range File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/series/vseries_command.py"", line 189, in vseries_save s = series[0] See log for complete Python traceback. > vseries slider #1 Traceback (most recent call last): File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/series/slider.py"", line 142, in play_cb self.play() File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/series/slider.py"", line 148, in play s0 = ser[0] IndexError: list index out of range IndexError: list index out of range File ""/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/series/slider.py"", line 148, in play s0 = ser[0] See log for complete Python traceback. OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103 OpenGL renderer: NVIDIA GeForce GT 750M OpenGL Engine OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Volume Data duplicate Tom Goddard all ChimeraX