Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#8085 closed defect (duplicate)

Modeller target is None

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.5rc202211171732 (2022-11-17 17:32:15 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5rc202211171732 (2022-11-17)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open pdb:2ZVW format mmcif fromDatabase pdb

2zvw title:  
Crystal structure of Proliferating cell nuclear antigen 2 and Short peptide
from human P21 [more info...]  
  
Chain information for 2zvw #1  
---  
Chain | Description | UniProt  
A B C D E F G H | Proliferating cell nuclear antigen 2 | PCNA2_ARATH  
I J K L M N O P | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvw #1  
---  
SO4 — sulfate ion  
  
2zvw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> close session

> open D:\Downloads\LjPCNA1.fa format fasta

Summary of feedback from opening D:\Downloads\LjPCNA1.fa  
---  
note | Alignment identifier is LjPCNA1.fa  
  
Opened 1 sequences from LjPCNA1.fa  

> blastprotein LjPCNA1.fa:1

Webservices job id: HCI2GBQZ0D0L1U7P  

> open pdb:6O09

Summary of feedback from opening 6O09 fetched from pdb  
---  
note | Fetching compressed mmCIF 6o09 from
http://files.rcsb.org/download/6o09.cif  
  
6o09 title:  
Structure of AtPCNA in complex with the PIP motif of ATXR6 [more info...]  
  
Chain information for 6o09 #1  
---  
Chain | Description | UniProt  
A C D F H K | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
B E G I J L | Uncharacterized protein | K7MRE7_SOYBN  
  
6o09 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> select clear

> close session

> open D:\Downloads\LjPCNA1.fa format fasta

Summary of feedback from opening D:\Downloads\LjPCNA1.fa  
---  
note | Alignment identifier is LjPCNA1.fa  
  
Opened 1 sequences from LjPCNA1.fa  

> blastprotein LjPCNA1.fa:1

Webservices job id: HT5LGIFONB3A9JFX  

> open pdb:2ZVV

Summary of feedback from opening 2ZVV fetched from pdb  
---  
note | Fetching compressed mmCIF 2zvv from
http://files.rcsb.org/download/2zvv.cif  
  
2zvv title:  
Crystal structure of Proliferating cellular nuclear antigen 1 and Short
peptide from human P21 [more info...]  
  
Chain information for 2zvv #1  
---  
Chain | Description | UniProt  
A B | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
X Y | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvv #1  
---  
SO4 — sulfate ion  
  
2zvv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> select clear

> close session

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  

> open D:\Downloads\LjPCNA1.fa format fasta

Summary of feedback from opening D:\Downloads\LjPCNA1.fa  
---  
note | Alignment identifier is LjPCNA1.fa  
  
Opened 1 sequences from LjPCNA1.fa  

> open pdb:2ZVV format mmcif fromDatabase pdb

2zvv title:  
Crystal structure of Proliferating cellular nuclear antigen 1 and Short
peptide from human P21 [more info...]  
  
Chain information for 2zvv #1  
---  
Chain | Description | UniProt  
A B | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
X Y | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvv #1  
---  
SO4 — sulfate ion  
  
2zvv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> close session

> ui tool show "Modeller Comparative"

> open pdb:2ZVV format mmcif fromDatabase pdb

2zvv title:  
Crystal structure of Proliferating cellular nuclear antigen 1 and Short
peptide from human P21 [more info...]  
  
Chain information for 2zvv #1  
---  
Chain | Description | UniProt  
A B | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
X Y | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvv #1  
---  
SO4 — sulfate ion  
  
2zvv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> open pdb:2ZVV format mmcif fromDatabase pdb

2zvv title:  
Crystal structure of Proliferating cellular nuclear antigen 1 and Short
peptide from human P21 [more info...]  
  
Chain information for 2zvv #2  
---  
Chain | Description | UniProt  
A B | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
X Y | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvv #2  
---  
SO4 — sulfate ion  
  
2zvv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> open D:\Downloads\LjPCNA1.fa format fasta

Summary of feedback from opening D:\Downloads\LjPCNA1.fa  
---  
note | Alignment identifier is LjPCNA1.fa  
  
Opened 1 sequences from LjPCNA1.fa  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1049+0+35 (frame:
1942x1105-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1046+0+34 (frame: 1942x1102-11-11) margins: 11, 45,
11, 11 minimum size: 511x699 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=789,
y=1105)))  

> open pdb:2ZVV format mmcif fromDatabase pdb

2zvv title:  
Crystal structure of Proliferating cellular nuclear antigen 1 and Short
peptide from human P21 [more info...]  
  
Chain information for 2zvv #3  
---  
Chain | Description | UniProt  
A B | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
X Y | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvv #3  
---  
SO4 — sulfate ion  
  
2zvv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> modeller comparative LjPCNA1.fa:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Alignment LjPCNA1.fa has no associated chains  

> open pdb:2ZVV format mmcif fromDatabase pdb

2zvv title:  
Crystal structure of Proliferating cellular nuclear antigen 1 and Short
peptide from human P21 [more info...]  
  
Chain information for 2zvv #4  
---  
Chain | Description | UniProt  
A B | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
X Y | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvv #4  
---  
SO4 — sulfate ion  
  
2zvv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> open pdb:2ZVV format mmcif fromDatabase pdb

2zvv title:  
Crystal structure of Proliferating cellular nuclear antigen 1 and Short
peptide from human P21 [more info...]  
  
Chain information for 2zvv #5  
---  
Chain | Description | UniProt  
A B | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
X Y | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvv #5  
---  
SO4 — sulfate ion  
  
2zvv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> log metadata #5

Metadata for 2zvv #5  
---  
Title | Crystal structure of Proliferating cellular nuclear antigen 1 and
Short peptide from human P21  
Citation | Strzalka, W., Oyama, T., Tori, K., Morikawa, K. (2009). Crystal
structures of the Arabidopsis thaliana proliferating cell nuclear antigen 1
and 2 proteins complexed with the human p21 C-terminal segment. Protein Sci.,
18, 1072-1080. PMID: 19388052. DOI: 10.1002/pro.117  
Non-standard residue | SO4 — sulfate ion  
Gene source | Arabidopsis thaliana (mouse-ear cress,thale-cress)  
Experimental method | X-ray diffraction  
Resolution | 2.00Å  
  
> open pdb:2ZVV format mmcif fromDatabase pdb

2zvv title:  
Crystal structure of Proliferating cellular nuclear antigen 1 and Short
peptide from human P21 [more info...]  
  
Chain information for 2zvv #6  
---  
Chain | Description | UniProt  
A B | Proliferating cellular nuclear antigen 1 | PCNA1_ARATH  
X Y | Cyclin-dependent kinase inhibitor 1 | CDN1A_HUMAN  
  
Non-standard residues in 2zvv #6  
---  
SO4 — sulfate ion  
  
2zvv mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> blastprotein LjPCNA1.fa:1

Webservices job id: YUN2VPZ9XRVOH884  
Alignment identifier is bp3 [1]  
Associated 2zvv chain A to 2ZVV_A with 0 mismatches  
Associated 2zvv chain B to 2ZVV_A with 0 mismatches  
Associated 2zvv chain A to 2ZVV_A with 0 mismatches  
Associated 2zvv chain B to 2ZVV_A with 0 mismatches  
Associated 2zvv chain A to 2ZVV_A with 0 mismatches  
Associated 2zvv chain B to 2ZVV_A with 0 mismatches  
Associated 2zvv chain A to 2ZVV_A with 0 mismatches  
Associated 2zvv chain B to 2ZVV_A with 0 mismatches  
Associated 2zvv chain A to 2ZVV_A with 0 mismatches  
Associated 2zvv chain B to 2ZVV_A with 0 mismatches  
Associated 2zvv chain A to 2ZVV_A with 0 mismatches  
Associated 2zvv chain B to 2ZVV_A with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment bp3 [1]  

> sequence identity "bp3 [1]:1" "bp3 [1]:2"

query vs. 2ZVV_A: 89.95% identity  

> ui tool show "Modeller Comparative"

> modeller comparative "bp3 [1]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\tool.py", line 302, in launch_modeller  
run(  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp3 [1]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\tool.py", line 302, in launch_modeller  
run(  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative LjPCNA1.fa:1 numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Alignment LjPCNA1.fa has no associated chains  

> modeller comparative "bp3 [1]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\tool.py", line 302, in launch_modeller  
run(  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp3 [1]:2" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\tool.py", line 302, in launch_modeller  
run(  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  

> modeller comparative "bp3 [1]:1" numModels 2 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\tool.py", line 302, in launch_modeller  
run(  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\cmd.py", line 37, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
AttributeError: 'NoneType' object has no attribute 'name'  
  
AttributeError: 'NoneType' object has no attribute 'name'  
  
File "C:\Users\Sebastian\OneDrive\Studium\ChimeraX\bin\lib\site-
packages\chimerax\modeller\comparative.py", line 160, in model  
target_name = "target" if len(targets) > 1 else target.name  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 526.98
OpenGL renderer: NVIDIA GeForce GTX 960/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: de_DE.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 17,095,184,384
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-4460  CPU @ 3.20GHz
OSLanguage: de-DE

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202211171732
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.0.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.32
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.10.0

Change History (3)

comment:1 by pett, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Sequence
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Modeller target is None

comment:2 by pett, 3 years ago

Resolution: → duplicate
Status: accepted → closed

This a duplicate of #7992 and is fixed on the develop branch. Should I cherry pick the fix onto the release branch?

comment:3 by Tom Goddard, 3 years ago

Not sure anyone can advise on whether the fix should go in 1.5 since we don't know how serious the bug is nor how dangerous the fix is. You decide.

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