Opened 2 years ago

Closed 2 years ago

#10021 closed defect (duplicate)

ISOLDE: swap_equivalent_atoms: different number of atoms being swapped

Reported by: alzbetmail@… 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 Eric Pettersen, 2 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: swap_equivalent_atoms: different number of atoms being swapped

Reported by Alzbeta

comment:2 by Tristan Croll, 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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