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Opened 6 years ago
Closed 6 years ago
#3024 closed defect (fixed)
'cartoon' command: 'Atoms' object has no attribute 'evaluate'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Tristan Croll, chimera-programmers | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Change History (7)
comment:1 by , 6 years ago
| Component: | Unassigned → Depiction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'cartoon' command: 'Atoms' object has no attribute 'evaluate' |
comment:2 by , 6 years ago
| Cc: | added |
|---|
comment:3 by , 6 years ago
Maybe after a release such as 0.92 the ChimeraX core version needs to be bumped to 0.93.dev1 and not 0.93 so that Toolshed bundles can guarantee they get a specific final release. Currently we have dozens of prerelease daily builds with the same version number as the final release.
comment:4 by , 6 years ago
I've been looking into this. We have daily, release candidate, and production builds. I propose that we use 0.94a202004031434, 0.94rc202004031434, and 0.94 for the version style. The 202004031434 is the date and time of the last change on branch, so releases would be ordered by version. 0.94.dev202004031434 would work too. PEP 440 details what is permitted. Right now, I'm using 2020-04-03 to version the daily build filenames -- would probably switch to whatever we decide.
follow-up: 5 comment:5 by , 6 years ago
Since our daily builds are primarily development builds I think 0.94.dev202004031434 is best. It is pretty ugly with the date stamp but I don't think it matters. In the ChimeraX log it might be better to beautify it a bit saying "0.94 daily 2020-04-03" as we do now with the "daily" added to make it clear this is a release version. Let's bring this up at today's group meeting.
comment:7 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
We will start using version numbers like 0.94.dev202004031434 for daily builds. Greg Couch said he will make this change.
This will prevent running ISOLDE with an incorrect ChimeraX version starting in the future.
Note:
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This error is because a ChimeraX older than release 0.93 is being used with Toolshed Clipper that requires 0.93 (core==0.93). In this bug report ChimeraX reports its version as 0.93 (3-24-2020) but the official 0.93 release did not come out until 4-3-2020.
Clipper and ISOLDE Toolshed bundles are intended to run with an exact production release ChimeraX version. Can bundle_info.xml specify a dependency that only gets a ChimeraX release version and not the daily build versions between 0.92 release and 0.93 release? Greg? Conrad?