id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3024 'cartoon' command: 'Atoms' object has no attribute 'evaluate' chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-91-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.93 (2020-03-24) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.93 (2020-03-24) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0b5-cp37-cp37m-linux_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing ./.cache/ChimeraX/0.93/installers/ChimeraX_ISOLDE-1.0b5-cp37-cp37m-linux_x86_64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages (from ChimeraX- ISOLDE==1.0b5) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Clipper==0.12.* in ./.local/share/ChimeraX/0.93/site-packages (from ChimeraX-ISOLDE==1.0b5) (0.12.0) Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.93 in /usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages (from ChimeraX- ISOLDE==1.0b5) (0.93) Requirement already satisfied, skipping upgrade: ChimeraX-Graphics>=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages (from ChimeraX- Atomic>=1.0->ChimeraX-ISOLDE==1.0b5) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Geometry>=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages (from ChimeraX- Atomic>=1.0->ChimeraX-ISOLDE==1.0b5) (1.0) Installing collected packages: ChimeraX-ISOLDE Attempting uninstall: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.0b5 Uninstalling ChimeraX-ISOLDE-1.0b5: Successfully uninstalled ChimeraX-ISOLDE-1.0b5 Successfully installed ChimeraX-ISOLDE-1.0b5 Lock 140193876513808 acquired on /home/golcukm/.cache/ChimeraX/0.93/toolshed/bundle_info.cache.lock Lock 140193876513808 released on /home/golcukm/.cache/ChimeraX/0.93/toolshed/bundle_info.cache.lock > open /home/golcukm/Downloads/6m0j-sf.cif > open /home/golcukm/Downloads/6m0j-sf.cif > open /home/golcukm/Downloads/6m0j_phases.mtz Must specify a structure model to associate with crystallographic data > open ""/home/golcukm/Downloads/6m0j (1).pdb"" 6m0j (1).pdb title: Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2 [more info...] Chain information for 6m0j (1).pdb #1 --- Chain | Description A | angiotensin-converting enzyme 2 E | sars-cov-2 receptor-binding domain Non-standard residues in 6m0j (1).pdb #1 --- CL — chloride ion NAG — N-acetyl-D-glucosamine ZN — zinc ion > open /home/golcukm/Downloads/6m0j_phases.mtz Must specify a structure model to associate with crystallographic data > toolshed show ISOLDE > set selectionWidth 4 6m0j (1).pdb title: Crystal structure of sars-cov-2 spike receptor-binding domain bound with ACE2 [more info...] Chain information for 6m0j (1).pdb --- Chain | Description 1.2/A | angiotensin-converting enzyme 2 1.2/E | sars-cov-2 receptor-binding domain Non-standard residues in 6m0j (1).pdb #1.2 --- CL — chloride ion NAG — N-acetyl-D-glucosamine ZN — zinc ion Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-cispro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-transpro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-gly-sym data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-prepro-noGP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-ileval-nopreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rama8000-general-noGPIVpreP data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/symmetry.py"", line 1214, in _set_default_cartoon_cb set_to_default_cartoon(self.session, model = self.structure) File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/clipper/util.py"", line 55, in set_to_default_cartoon cartoon.cartoon(session, atoms = atoms, suppress_backbone_display=False) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/std_commands/cartoon.py"", line 71, in cartoon results = atoms.evaluate(session) AttributeError: 'Atoms' object has no attribute 'evaluate' Error processing trigger ""frame drawn"": AttributeError: 'Atoms' object has no attribute 'evaluate' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/std_commands/cartoon.py"", line 71, in cartoon results = atoms.evaluate(session) See log for complete Python traceback. Done loading forcefield Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/validation/rama_annotation.py"", line 222, in _update_graphics_if_needed self.update_graphics() File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/validation/rama_annotation.py"", line 234, in update_graphics coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas, self.hide_favored) File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 1067, in _ca_positions_colors_and_selecteds pointer(coords), pointer(colors), pointer(selecteds)) TypeError: All atoms must be in the same structure! Error processing trigger ""changes"": TypeError: All atoms must be in the same structure! File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 1067, in _ca_positions_colors_and_selecteds pointer(coords), pointer(colors), pointer(selecteds)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/validation/rama_annotation.py"", line 222, in _update_graphics_if_needed self.update_graphics() File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/validation/rama_annotation.py"", line 234, in update_graphics coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas, self.hide_favored) File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 1067, in _ca_positions_colors_and_selecteds pointer(coords), pointer(colors), pointer(selecteds)) TypeError: All atoms must be in the same structure! Error processing trigger ""changes"": TypeError: All atoms must be in the same structure! File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 1067, in _ca_positions_colors_and_selecteds pointer(coords), pointer(colors), pointer(selecteds)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/validation/rama_annotation.py"", line 222, in _update_graphics_if_needed self.update_graphics() File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/validation/rama_annotation.py"", line 234, in update_graphics coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas, self.hide_favored) File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 1067, in _ca_positions_colors_and_selecteds pointer(coords), pointer(colors), pointer(selecteds)) TypeError: All atoms must be in the same structure! Error processing trigger ""changes"": TypeError: All atoms must be in the same structure! File ""/home/golcukm/.local/share/ChimeraX/0.93/site- packages/chimerax/isolde/molobject.py"", line 1067, in _ca_positions_colors_and_selecteds pointer(coords), pointer(colors), pointer(selecteds)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 435.21 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Micro-Star International Co., Ltd. Model: GE63VR 7RF OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz Cache Size: 6144 KB Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:591b] (rev 04) Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:11f7] Kernel driver in use: i915 }}} " defect closed normal Depiction fixed Tristan Croll chimera-programmers all ChimeraX