Opened 2 years ago
Closed 2 years ago
#10021 closed defect (duplicate)
ISOLDE: swap_equivalent_atoms: different number of atoms being swapped
Reported by: | Owned by: | Tristan Croll | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Third Party | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.13.6-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. > open /Users/alzbetka/Desktop/session_Isolda.cxs Opened RRR_template.mrc as #2, grid size 380,380,380, pixel 0.834, shown at level 0.176, step 2, values float32 Log from Thu Oct 19 11:06:26 2023UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/alzbetka/Desktop/RRR_template2.pdb Summary of feedback from opening /Users/alzbetka/Desktop/RRR_template2.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 5 ASN A 13 1 9 Start residue of secondary structure not found: HELIX 2 2 GLN A 19 LEU A 29 1 11 Start residue of secondary structure not found: HELIX 3 3 LEU A 30 ASP A 35 1 6 Start residue of secondary structure not found: HELIX 4 4 ALA A 36 LEU A 48 1 13 Start residue of secondary structure not found: HELIX 5 5 THR A 54 GLY A 73 1 20 14 messages similar to the above omitted Chain information for RRR_template2.pdb --- Chain | Description 1.1/A | No description available 1.2/A | No description available 1.2/B | No description available > set bgColor white > ui mousemode right select Drag select of 1429 residues, 8 pseudobonds, 26 atoms, 21 bonds > show sel cartoons > graphics silhouettes true > color sel bychain > hide #!1.1 models > show #!1.1 models > color #1.1 #fffb00 transparency 0 > select clear > select #1.1 6398 atoms, 6477 bonds, 67 pseudobonds, 409 residues, 2 models selected > ~select #1.1 Nothing selected > select #1.1 6398 atoms, 6477 bonds, 67 pseudobonds, 409 residues, 2 models selected > color #1.1 #00fa92 transparency 0 > select #1.2 15411 atoms, 15613 bonds, 7 pseudobonds, 1021 residues, 2 models selected Alignment identifier is 1.2/A Alignment identifier is 1.2/B > select #1.2/B:1 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1.2/B:1-929 9638 atoms, 9781 bonds, 6 pseudobonds, 651 residues, 2 models selected > color (#!1.2 & sel) yellow > select #1.2/A:377-379 41 atoms, 41 bonds, 3 residues, 1 model selected > select #1.2/A:1-379 5635 atoms, 5693 bonds, 1 pseudobond, 362 residues, 2 models selected > color (#!1.2 & sel) hot pink > select clear Drag select of 22 residues > select #1.2/A:386 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1.2/A:376-386 189 atoms, 191 bonds, 11 residues, 1 model selected > color sel hot pink > select clear > select #1.2/A:14 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1.2/A:14-19 68 atoms, 67 bonds, 6 residues, 1 model selected > color sel orange > select #1.2/A:19 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1.2/A:19 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > select #1.1 6398 atoms, 6477 bonds, 67 pseudobonds, 409 residues, 2 models selected Alignment identifier is 1.1/A > select #1.1/A:260-261 33 atoms, 33 bonds, 2 residues, 1 model selected > select #1.1/A:260-265 99 atoms, 100 bonds, 6 residues, 1 model selected > color sel orange > select #1.1/A:269 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1.1/A:269-270 24 atoms, 23 bonds, 2 residues, 1 model selected > color sel red > select clear > open /Users/alzbetka/Desktop/RRR_template.mrc Opened RRR_template.mrc as #2, grid size 380,380,380, pixel 0.834, shown at level 0.176, step 2, values float32 > select #2 2 models selected > ui mousemode right "rotate selected models" > ui mousemode right "translate selected models" > view matrix models #2,1,0,0,10.62,0,1,0,-134.4,0,0,1,-106.46 > view matrix models #2,1,0,0,-64.661,0,1,0,-178.92,0,0,1,-144.04 > ui mousemode right "rotate selected models" > view matrix models > #2,-0.38489,0.89915,-0.20832,21.858,-0.57147,-0.054929,0.81878,-59.447,0.72476,0.43419,0.53498,-242.47 > view matrix models > #2,-0.82334,-0.53044,-0.20186,313.37,-0.26456,0.04404,0.96336,-142.44,-0.50212,0.84658,-0.17659,-19.189 > view matrix models > #2,-0.81191,-0.58193,0.046458,280.06,0.064386,-0.010166,0.99787,-186.22,-0.58022,0.81317,0.045722,-38.454 > surface dust #2 size 8.34 > ui mousemode right "rotate selected models" > view matrix models > #2,-0.32198,-0.94042,0.10926,257.7,0.14936,0.063503,0.98674,-208.41,-0.93489,0.33403,0.12001,77.285 > view matrix models > #2,0.93222,-0.36146,-0.017848,6.0358,0.13365,0.29801,0.94516,-237.2,-0.33632,-0.88348,0.32612,154.55 > view matrix models > #2,0.91934,0.37391,-0.12247,-93.59,-0.017997,0.35091,0.93624,-222.63,0.39304,-0.85852,0.32934,45.934 > ui mousemode right "translate selected models" > view matrix models > #2,0.91934,0.37391,-0.12247,-191.42,-0.017997,0.35091,0.93624,-214.55,0.39304,-0.85852,0.32934,91.729 > view matrix models > #2,0.91934,0.37391,-0.12247,-195.54,-0.017997,0.35091,0.93624,-216.62,0.39304,-0.85852,0.32934,93.317 > view matrix models > #2,0.91934,0.37391,-0.12247,-220.67,-0.017997,0.35091,0.93624,-214.55,0.39304,-0.85852,0.32934,60.767 > color #2 #ff40ff models transparency 0 > color #2 #ff40ff43 models > view matrix models > #2,0.91934,0.37391,-0.12247,-219.37,-0.017997,0.35091,0.93624,-214.71,0.39304,-0.85852,0.32934,60.433 > view matrix models > #2,0.91934,0.37391,-0.12247,-219.79,-0.017997,0.35091,0.93624,-213.59,0.39304,-0.85852,0.32934,60.804 > color #2 #ff40ff42 models > view matrix models > #2,0.91934,0.37391,-0.12247,-216.12,-0.017997,0.35091,0.93624,-214.4,0.39304,-0.85852,0.32934,51.604 > ui mousemode right "rotate selected models" > view matrix models > #2,0.63381,-0.77346,0.0069889,-11.627,0.18599,0.16117,0.96924,-218.3,-0.7508,-0.61301,0.246,188.76 > ui mousemode right "translate selected models" > view matrix models > #2,0.63381,-0.77346,0.0069889,-15.234,0.18599,0.16117,0.96924,-219.55,-0.7508,-0.61301,0.246,201.75 > view matrix models > #2,0.63381,-0.77346,0.0069889,-15.158,0.18599,0.16117,0.96924,-219.41,-0.7508,-0.61301,0.246,201.18 > ui tool show ISOLDE > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Traceback (most recent call last): File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 554, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py", line 1264, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/__init__.py", line 155, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tools.py", line 193, in get_singleton tinst = tool_class(session, tool_name, **kw) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/tool.py", line 186, in __init__ self.isolde = isolde.Isolde(self) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py", line 317, in __init__ self._start_gui(gui) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py", line 482, in _start_gui self._update_model_list(None, None, force=True) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py", line 1050, in _update_model_list self._change_selected_model(model=current_model) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py", line 2525, in _change_selected_model correct_pseudosymmetric_sidechain_atoms(session, m.residues) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/atomic/util.py", line 28, in correct_pseudosymmetric_sidechain_atoms if flip_if_necessary(r, ('CD','NE','CZ',('NH2','NH1'))): File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/atomic/util.py", line 66, in flip_if_necessary if swap_equivalent_atoms(residue): File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/atomic/util.py", line 118, in swap_equivalent_atoms pair[0].coords, pair[1].coords = pair[1].coords, pair[0].coords File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' ValueError: Values array length 3 does not match objects array length 4 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 1659, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py", line 2856, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show bi.start_tool(session, name) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 559, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Values array length 3 does not match objects array length 4 chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Values array length 3 does not match objects array length 4 File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 559, in start_tool raise ToolshedError( See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 2251, in <lambda> dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 654, in close_request tool_instance.delete() File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/tool.py", line 191, in delete self.isolde._on_close() AttributeError: 'ISOLDE_ToolUI' object has no attribute 'isolde' AttributeError: 'ISOLDE_ToolUI' object has no attribute 'isolde' File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/tool.py", line 191, in delete self.isolde._on_close() See log for complete Python traceback. > save /Users/alzbetka/Desktop/session_Isolda.cxs ——— End of log from Thu Oct 19 11:06:26 2023 ——— opened ChimeraX session > ui tool show ISOLDE > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Traceback (most recent call last): File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 554, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/__init__.py", line 1264, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/__init__.py", line 155, in start_tool return tools.get_singleton(session, ISOLDE_ToolUI, 'ISOLDE', create=True) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/tools.py", line 193, in get_singleton tinst = tool_class(session, tool_name, **kw) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/tool.py", line 186, in __init__ self.isolde = isolde.Isolde(self) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py", line 317, in __init__ self._start_gui(gui) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py", line 482, in _start_gui self._update_model_list(None, None, force=True) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py", line 1050, in _update_model_list self._change_selected_model(model=current_model) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/isolde.py", line 2525, in _change_selected_model correct_pseudosymmetric_sidechain_atoms(session, m.residues) File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/atomic/util.py", line 28, in correct_pseudosymmetric_sidechain_atoms if flip_if_necessary(r, ('CD','NE','CZ',('NH2','NH1'))): File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/atomic/util.py", line 66, in flip_if_necessary if swap_equivalent_atoms(residue): File "/Users/alzbetka/Library/Application Support/ChimeraX/1.3/site- packages/chimerax/isolde/atomic/util.py", line 118, in swap_equivalent_atoms pair[0].coords, pair[1].coords = pair[1].coords, pair[0].coords File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/atomic/molc.py", line 210, in set_prop raise ValueError('Values array length %d does not match objects array length %d' ValueError: Values array length 3 does not match objects array length 4 During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/gui.py", line 1659, in <lambda> run(ses, "ui tool show %s" % StringArg.unparse(tool_name))) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py", line 2856, in run result = ci.function(session, **kw_args) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/cmd.py", line 219, in ui_tool_show bi.start_tool(session, name) File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 559, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Values array length 3 does not match objects array length 4 chimerax.core.toolshed.ToolshedError: start_tool() failed for tool ISOLDE in bundle ChimeraX-ISOLDE: Values array length 3 does not match objects array length 4 File "/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/toolshed/info.py", line 559, in start_tool raise ToolshedError( See log for complete Python traceback. OpenGL version: 4.1 INTEL-10.36.19 OpenGL renderer: Intel(R) HD Graphics 6000 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir7,2 Processor Name: Intel Core i5 Processor Speed: 1,8 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Memory: 8 GB Boot ROM Version: 195.0.0.0.0 SMC Version (system): 2.27f2 Software: System Software Overview: System Version: macOS 10.13.6 (17G66) Kernel Version: Darwin 17.7.0 Time since boot: 16 days 21:39 Graphics/Displays: Intel HD Graphics 6000: Chipset Model: Intel HD Graphics 6000 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1626 Revision ID: 0x0009 Metal: Supported, feature set macOS GPUFamily1 v3 Displays: Color LCD: Display Type: LCD Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus) UI Looks like: 1440 x 900 Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DisplayPort LED Cinema Display: Display Type: LCD Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: 2A9381810K0 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Connection Type: DisplayPort Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 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: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0
Change History (2)
comment:1 by , 2 years ago
Component: | Unassigned → Third Party |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → ISOLDE: swap_equivalent_atoms: different number of atoms being swapped |
comment:2 by , 2 years ago
Resolution: | → duplicate |
---|---|
Status: | assigned → closed |
This should be fixed if you upgrade to ISOLDE 1.6 (by updating ChimeraX to 1.6 and reinstalling ISOLDE).
Note:
See TracTickets
for help on using tickets.
Reported by Alzbeta