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Opened 7 years ago
Last modified 7 years ago
#1713 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-17.7.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-02-08) Description Reproducer: close; open pdb:1tbq; getcrd /K:187@CA Log: UCSF ChimeraX version: 0.9 (2019-02-08) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open CD20_Ritux.cxc > open /Users/rohoua/work/Genentech/CD20/CD20_Ritux/CD20_Ritux_190208_new_Fc_noH2O_asym_BIOMT_BIOMT_expanded_real_space_refined_edited3-coot-1.pdb name '"atomic model"' Summary of feedback from opening /Users/rohoua/work/Genentech/CD20/CD20_Ritux/CD20_Ritux_190208_new_Fc_noH2O_asym_BIOMT_BIOMT_expanded_real_space_refined_edited3-coot-1.pdb --- warnings | Ignored bad PDB record found on line 22 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 23 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 24 BOND : 0.010 0.065 9358 Ignored bad PDB record found on line 25 ANGLE : 1.092 13.638 12736 Ignored bad PDB record found on line 26 CHIRALITY : 0.065 0.341 1444 16 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (87 ) Cannot find LINK/SSBOND residue CYS (133 ) Cannot find LINK/SSBOND residue CYS (96 ) Cannot find LINK/SSBOND residue CYS (148 ) Cannot find LINK/SSBOND residue CYS (87 ) 3 messages similar to the above omitted Chain information for atomic model #1 --- Chain | Description C D | No description available H I | No description available L M | No description available > open /Users/rohoua/work/Genentech/CD20/CD20_Ritux/181217_CD20_interim_results/generate3d_volume_28_31_1_sharp_8_4p0_m90_0_20_fom_z.mrc name '"map"' Opened generate3d_volume_28_31_1_sharp_8_4p0_m90_0_20_fom_z.mrc, grid size 310,310,310, pixel 1, shown at level 0.0611, step 2, values float32 > open /Users/rohoua/work/Genentech/CD20/CD20_Ritux/181217_CD20_interim_results/generate3d_volume_28_31_1_sharp_8_3p12_m90_0_20_fom_z.mrc name '"map sharp"' Opened generate3d_volume_28_31_1_sharp_8_3p12_m90_0_20_fom_z.mrc, grid size 310,310,310, pixel 1, shown at level 0.0816, step 2, values float32 > name cd20RituxDimer #1 > name cd20 #1/C,D > name cd20Monomer #1/C > name cd20H1 #1/C,D:46-70 > name cd20ECL1 #1/C,D:71-81 > name cd20H2 #1/C,D:82-105 > name cd20ICL1 #1/C,D:106-112 > name cd20H3 #1/C,D:113-140 > name cd20ECL2 #1/C,D:141-182 > name cd20ECL2SS #1/C,D:167,183 > name cd20H4 #1/C,D:183-207 > name cd20DimerInt #1/C,D:62,200,65,196,69,192,73,188,76,185,58,54,50 > name Ritux #1/H,L,I,M > name RituxH #1/H,I > name RituxL #1/L,M > name RituxEpitope #1/C,D:168-175 > set bgColor white > set silhouettes true > lighting full > open CD20_Ritux_color_model.cxc > color cd20RituxDimer gray > color cd20 burlywood > color modify cd20H1 hue - 20 > color modify cd20H2 hue - 10 > color modify cd20H3 hue + 0 > color modify cd20H4 hue + 10 > color modify cd20ECL1 hue +10 > color modify cd20ECL2 hue + 40 > color modify cd20 saturation + 80 > color Ritux plum > color modify RituxH hue - 40 executed CD20_Ritux_color_model.cxc > hide cd20RituxDimer > ribbon cd20RituxDimer > show cd20ECL2SS > style cd20ECL2SS stick Changed 24 atom styles > volume zone #2 nearAtoms Ritux range 10.0 invert true newMap true modelId 100 > volume zone #100 nearAtoms cd20 range 3.0 invert true newMap true modelId 4 > close #100 > volume #2 step 1 level 0.33 color #9999CC > volume #3 step 1 level 0.33 color #9999CC > volume #4 step 1 level 0.1 color #CCCCFF55 > display #2,4 > color zone #2 near cd20RituxDimer distance 4.0 > color zone #3 near cd20RituxDimer distance 4.0 > hide #!4 models > hide #!3 models > hide #!2 models > show #!1 models > turn x 90 executed CD20_Ritux.cxc > save /Users/rohoua/Desktop/image8.png supersample 3 > help scalebar No help found for 'scalebar' > help Developer warnings in user commands index: * didn't expect href to be to tools/sequenceviewer.html on line 246 > help distance > distance /L:213@CA /M:213@CA Distance between /L GLU 213 CA and /M GLU 213 CA: 142.962Å > turn y 90 > turn y 180 > view orient > view initial > open CD20_Ritux_overview_figures.cxc > close > open CD20_Ritux.cxc > open /Users/rohoua/work/Genentech/CD20/CD20_Ritux/CD20_Ritux_190208_new_Fc_noH2O_asym_BIOMT_BIOMT_expanded_real_space_refined_edited3-coot-1.pdb name '"atomic model"' Summary of feedback from opening /Users/rohoua/work/Genentech/CD20/CD20_Ritux/CD20_Ritux_190208_new_Fc_noH2O_asym_BIOMT_BIOMT_expanded_real_space_refined_edited3-coot-1.pdb --- warnings | Ignored bad PDB record found on line 22 GEOMETRY RESTRAINTS LIBRARY: CDL v1.2 Ignored bad PDB record found on line 23 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 24 BOND : 0.010 0.065 9358 Ignored bad PDB record found on line 25 ANGLE : 1.092 13.638 12736 Ignored bad PDB record found on line 26 CHIRALITY : 0.065 0.341 1444 16 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (87 ) Cannot find LINK/SSBOND residue CYS (133 ) Cannot find LINK/SSBOND residue CYS (96 ) Cannot find LINK/SSBOND residue CYS (148 ) Cannot find LINK/SSBOND residue CYS (87 ) 3 messages similar to the above omitted Chain information for atomic model #1 --- Chain | Description C D | No description available H I | No description available L M | No description available > open /Users/rohoua/work/Genentech/CD20/CD20_Ritux/181217_CD20_interim_results/generate3d_volume_28_31_1_sharp_8_4p0_m90_0_20_fom_z.mrc name '"map"' Opened generate3d_volume_28_31_1_sharp_8_4p0_m90_0_20_fom_z.mrc, grid size 310,310,310, pixel 1, shown at level 0.0611, step 2, values float32 > open /Users/rohoua/work/Genentech/CD20/CD20_Ritux/181217_CD20_interim_results/generate3d_volume_28_31_1_sharp_8_3p12_m90_0_20_fom_z.mrc name '"map sharp"' Opened generate3d_volume_28_31_1_sharp_8_3p12_m90_0_20_fom_z.mrc, grid size 310,310,310, pixel 1, shown at level 0.0816, step 2, values float32 > name cd20RituxDimer #1 > name cd20 #1/C,D > name cd20Monomer #1/C > name cd20H1 #1/C,D:46-70 > name cd20ECL1 #1/C,D:71-81 > name cd20H2 #1/C,D:82-105 > name cd20ICL1 #1/C,D:106-112 > name cd20H3 #1/C,D:113-140 > name cd20ECL2 #1/C,D:141-182 > name cd20ECL2SS #1/C,D:167,183 > name cd20H4 #1/C,D:183-207 > name cd20DimerInt #1/C,D:62,200,65,196,69,192,73,188,76,185,58,54,50 > name Ritux #1/H,L,I,M > name RituxH #1/H,I > name RituxL #1/L,M > name RituxEpitope #1/C,D:168-175 > set bgColor white > set silhouettes true > lighting full > open CD20_Ritux_color_model.cxc > color cd20RituxDimer gray > color cd20 burlywood > color modify cd20H1 hue - 20 > color modify cd20H2 hue - 10 > color modify cd20H3 hue + 0 > color modify cd20H4 hue + 10 > color modify cd20ECL1 hue +10 > color modify cd20ECL2 hue + 40 > color modify cd20 saturation + 80 > color Ritux plum > color modify RituxH hue - 40 executed CD20_Ritux_color_model.cxc > hide cd20RituxDimer > ribbon cd20RituxDimer > show cd20ECL2SS > style cd20ECL2SS stick Changed 24 atom styles > volume zone #2 nearAtoms Ritux range 10.0 invert true newMap true modelId 100 > volume zone #100 nearAtoms cd20 range 3.0 invert true newMap true modelId 4 > close #100 > volume #2 step 1 level 0.33 color #9999CC > volume #3 step 1 level 0.33 color #9999CC > volume #4 step 1 level 0.1 color #CCCCFF55 > display #2,4 > color zone #2 near cd20RituxDimer distance 4.0 > color zone #3 near cd20RituxDimer distance 4.0 > hide #!4 models > hide #!3 models > hide #!2 models > show #!1 models > turn x 90 executed CD20_Ritux.cxc > save Figures/CD20_Ritux_overview_ribbons_wideside.png supersample 3 > turn y 90 > save Figures/CD20_Ritux_overview_ribbons_narrowside.png supersample 3 > turn y -90 > turn x 90 > save Figures/CD20_Ritux_overview_ribbons_top.png supersample 3 > turn x -180 > save Figures/CD20_Ritux_overview_ribbons_bottom.png supersample 3 > getcrd /L:213@CA model Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /L:213@CA 226.486 155.374 102.618 > getcrd /M:213@CA model Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /M:213@CA 83.526 154.639 102.618 > getcrd /H:16@CA model Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /H:16@CA 184.924 180.815 122.837 > getcrd /L:202@CA model Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /L:202@CA 210.607 133.184 116.113 > getcrd /H:191@CA model Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /H:191@CA 210.829 151.513 83.648 > getcrd /C:111@CA model Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /C:111@CA 167.859 144.657 197.098 executed CD20_Ritux_overview_figures.cxc > getcrd /L:213@CA model Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /L:213@CA 226.486 155.374 102.618 > getcrd /L:213@CA Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /L:213@CA 226.486 155.374 102.618 > help getcrd > close > open pdb:1tbq 1tbq title: Crystal structure of insect derived double domain kazal inhibitor rhodniin In complex with thrombin [more info...] Chain information for 1tbq #1 --- Chain | Description H K | thrombin J L | thrombin R S | rhodniin 1tbq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > getcrd /K:187@CA Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /K:187@CA 13.153 101.659 66.719 > select /K:187@CA 1 atom selected > getcrd /K:187@CA Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 50, in <lambda> data[0] == pself.attr_name and pself.set(pself.get_attribute())) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/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 "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/core_settings_ui.py", line 435, in _core_setting_changed self.options[setting_name].set(new_val) File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) ValueError: 'command-line specifier' is not in list Error processing trigger "setting changed": 'command-line specifier' is not in list: ValueError: 'command-line specifier' is not in list File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/options/options.py", line 606, in set self.widget.setText(self.labels[list(self.values).index(value)]) See log for complete Python traceback. Atom /K:187@CA 13.153 101.659 66.719 OpenGL version: 4.1 INTEL-10.36.23 OpenGL renderer: Intel(R) Iris(TM) Graphics 650 OpenGL vendor: Intel Inc.
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