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).
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Reported by Alzbeta